Alignments for a candidate for rocA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Magnetospirillum magneticum AMB-1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011384888.1 AMB_RS12610 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::HerbieS:HSERO_RS00905
         (1230 letters)



>NCBI__GCF_000009985.1:WP_011384888.1
          Length = 1039

 Score =  926 bits (2394), Expect = 0.0
 Identities = 534/1028 (51%), Positives = 668/1028 (64%), Gaps = 41/1028 (3%)

Query: 21   LPTPSPLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDATQQLARKLVQQVREKRTRSSG 80
            LP P P R AI  A    E + V  L   +  E   +      A  LV   R  R R+ G
Sbjct: 7    LPAPDPERQAIHRAAGTSEADLVSGLSAGIPLEDEARRRIVNRAVNLVDGARRNR-RTLG 65

Query: 81   VDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIADKISKGDWRKHLGESPSLFVN 140
            +D L++E+ LS+ EGV LMCLAEALLRIPD  T D LI DKI+  DW  HLG SPS+FVN
Sbjct: 66   LDGLLNEYRLSTREGVVLMCLAEALLRIPDDHTVDLLIKDKIASADWDGHLGHSPSVFVN 125

Query: 141  AATWGLLITGKLVSTSSESGLTQAITRLIGKGGEPLIRKGVDLAMRMLGNQFVTGQTIEE 200
            A+TW L++  +L+    +      + R+ G+ GE ++R+ +  AM ++G QFV G+TI E
Sbjct: 126  ASTWALVLGDRLLHLEEDG--RAVLGRMAGRLGEAVVRRALRHAMGLMGRQFVLGRTIAE 183

Query: 201  ALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESAIHAIGRASNGRGIKDGPGIS 260
            ALDN+R  E RGYR+S+DMLGEAA     A  Y ++Y  AI A+GR + G G   GPG+S
Sbjct: 184  ALDNARAWEARGYRHSFDMLGEAARCEQAAQDYLRAYAGAIEALGRHAKGAGPIAGPGLS 243

Query: 261  VKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGLNIDAEEADRLELSLDMMEVL 320
            VKLSALHPR+  AQ  RV+ EL+PRL+ L   A+   IGL IDAEEADRL++SLD+ME  
Sbjct: 244  VKLSALHPRFEMAQRQRVLGELVPRLRDLCHRARDAGIGLTIDAEEADRLDISLDVMEAA 303

Query: 321  VADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRRLMIRLVKGAYWDSEIKRAQV 380
            +ADP L G+DG G  VQ YQKR   VI +   LA R  +RLMIRLVKGAYWD E+KRAQ 
Sbjct: 304  LADPALDGWDGFGMAVQAYQKRARPVIAWAGALAARRQQRLMIRLVKGAYWDGEVKRAQE 363

Query: 381  DGLEGYPVYTRKVHTDLSYLTCAQKLLAATDVIYPQFATHNAHTLAAIYHWARQHQIDNY 440
             GL G+PV+T K  TD+SYL CA  LLA  D+ YPQFATHNAHT AA+          ++
Sbjct: 364  RGLGGFPVFTTKEATDVSYLACAADLLARPDLFYPQFATHNAHTAAAVMEMT--GGAGDW 421

Query: 441  EFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLAYLVRRLLENGANSSFVNQIV 500
            EFQ LHGMGE LY Q+V P+     CR YAPVGSHQ LL YLVRRLLENGANSSFV+++ 
Sbjct: 422  EFQRLHGMGEALYAQLV-PE---FPCRTYAPVGSHQELLPYLVRRLLENGANSSFVSRLA 477

Query: 501  DEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERKNSAGIDLSNEDRLQQLGQLF 560
            DE +P   +  DP+    A G +    +A P  L+G  R+NS G+DLS+   L QL    
Sbjct: 478  DEEIPAHVVAADPL---AALGRITPQLVAEPSALFGPSRRNSGGLDLSSPAVLAQLDLAL 534

Query: 561  ISMADRQWQAAPLLAADTAAQSAQAAQLVRNPADLREVVGQVSEATVADVDTALRAATDY 620
             ++A  + ++AP++  D   +  QAA+ V +PAD R VVG+V +A+ ADV+ AL +A   
Sbjct: 535  AAVATPE-RSAPIV--DGRERENQAAKPVLDPADHRRVVGEVVDASPADVEAALASARAA 591

Query: 621  APQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGKSLPNAIAEVREAVDFLRYYA 680
             P W       RA++LERAAD LE   A  MALA+REAGK++P+A++EVREAVDFLR+YA
Sbjct: 592  FPAWDDLGGEARASILERAADRLEADRARFMALAIREAGKTIPDALSEVREAVDFLRFYA 651

Query: 681  --IASRHDGNVLAWGPV--------------VCISPWNFPLAIFIGEVSAALAAGNVVLA 724
                +R    V   GPV               CISPWNFPLAIF+G+V+AALAAGN V+A
Sbjct: 652  AEARARFSQPVRLPGPVGESNELMLGGRGVFACISPWNFPLAIFVGQVAAALAAGNAVVA 711

Query: 725  KPAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGSTEVAQ 784
            KPA QT L+A  AV+LLH+AG+P  AL L+PG G  +G ALT +  V  + FTGST  A+
Sbjct: 712  KPAPQTPLMAAAAVRLLHQAGVPPQALHLVPG-GPAIGEALTVNPLVDAIAFTGSTATAR 770

Query: 785  LINRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFDSAGQ 844
             INR  A     DG         PLIAETGG NA+IVDSSAL EQVV D L SAF SAGQ
Sbjct: 771  HINRLRAAM---DGP------LAPLIAETGGLNAMIVDSSALPEQVVADCLESAFRSAGQ 821

Query: 845  RCSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDHIERM 904
            RCSALR+  +Q +   R   +L GAMAEL +G P  LS D+GPVID  +R+ LL H  R+
Sbjct: 822  RCSALRVAFIQREAWTRIQPLLAGAMAELSLGDPALLSTDVGPVIDEASRRRLLAHGGRL 881

Query: 905  RASARAVHQLPLGEECQHGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQLIDA 964
            R + R + Q     +C+ GTF AP   ++D+L  LQ EVFGP+LHV+ +    L Q++D 
Sbjct: 882  RHAGRMIGQSACPPDCRVGTFFAPMAHQLDNLDLLQSEVFGPILHVIPWEAGRLEQVLDC 941

Query: 965  INATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGTGPKA 1024
            + AT YGLTLG+HSRID TI  V  RA +GNIYVNR ++GAVVG QPFGG G SGTG KA
Sbjct: 942  VAATSYGLTLGIHSRIDATIAQVIARARIGNIYVNRTMIGAVVGSQPFGGLGLSGTGAKA 1001

Query: 1025 GGPLYLKR 1032
            GGP  L R
Sbjct: 1002 GGPNTLIR 1009



 Score = 38.9 bits (89), Expect = 2e-06
 Identities = 63/234 (26%), Positives = 86/234 (36%), Gaps = 51/234 (21%)

Query: 999  NRNIVGAVVGVQPFGGEGKSGTGPKA-------GGPLYLKRLQRNAQLHEE--------L 1043
            +R +VG VV   P   E    +   A       GG      L+R A   E          
Sbjct: 566  HRRVVGEVVDASPADVEAALASARAAFPAWDDLGGEARASILERAADRLEADRARFMALA 625

Query: 1044 TRAQPADVPNALLD--SLLDWARTHGHERLAANGQRYHRDSLLQRSLVLPGPTGERNTLG 1101
             R     +P+AL +    +D+ R +  E  A   Q             LPGP GE N L 
Sbjct: 626  IREAGKTIPDALSEVREAVDFLRFYAAEARARFSQPVR----------LPGPVGESNELM 675

Query: 1102 FAPRGLVLCAAG---SVGTLLNQLAAAFATGN---------TALVDERSAAIL-PSGLP- 1147
               RG+  C +     +   + Q+AAA A GN         T L+   +  +L  +G+P 
Sbjct: 676  LGGRGVFACISPWNFPLAIFVGQVAAALAAGNAVVAKPAPQTPLMAAAAVRLLHQAGVPP 735

Query: 1148 -----APVRAAIRRASQLDAEPLQAALV---DSHQAAHWRARLAAREGALVPLI 1193
                  P   AI  A  L   PL  A+     +  A H     AA +G L PLI
Sbjct: 736  QALHLVPGGPAIGEA--LTVNPLVDAIAFTGSTATARHINRLRAAMDGPLAPLI 787



 Score = 27.3 bits (59), Expect = 0.007
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 1203 LWRLLAERALCINTTAAGGNASLM 1226
            L R   ER L +NT AAGG+ +LM
Sbjct: 1007 LIRYGVERCLSVNTAAAGGDVALM 1030


Lambda     K      H
   0.319    0.134    0.389 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3106
Number of extensions: 164
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 1230
Length of database: 1039
Length adjustment: 46
Effective length of query: 1184
Effective length of database: 993
Effective search space:  1175712
Effective search space used:  1175712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)

Align candidate WP_011384888.1 AMB_RS12610 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01238.hmm
# target sequence database:        /tmp/gapView.27271.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-184  599.0   0.1   4.9e-184  598.4   0.1    1.2  1  lcl|NCBI__GCF_000009985.1:WP_011384888.1  AMB_RS12610 bifunctional proline


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384888.1  AMB_RS12610 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehy
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.4   0.1  4.9e-184  4.9e-184       2     495 ..     508    1010 ..     507    1014 .. 0.98

  Alignments for each domain:
  == domain 1  score: 598.4 bits;  conditional E-value: 4.9e-184
                                 TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqv 68  
                                                l+g +r+ns G+dl+   +l++l+  l ++a+ + ++apiv+++ ++++ a+pv +pad++ +vG+v
  lcl|NCBI__GCF_000009985.1:WP_011384888.1  508 LFGPSRRNSGGLDLSSPAVLAQLDLALAAVATPE-RSAPIVDGRERENQAAKPVLDPADHRRVVGEV 573 
                                                899**********************998887766.789***************************** PP

                                 TIGR01238   69 seadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaev 135 
                                                  a+ a+v++a+ sa aaf+ w  +  + ra+iler+ad le +   ++al++reaGkt+ +a++ev
  lcl|NCBI__GCF_000009985.1:WP_011384888.1  574 VDASPADVEAALASARAAFPAWDDLGGEARASILERAADRLEADRARFMALAIREAGKTIPDALSEV 640 
                                                ******************************************************************* PP

                                 TIGR01238  136 reavdflryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGn 189 
                                                reavdflr+ya +++  +++    +             +G++ cispwnfplaif+Gq+aaalaaGn
  lcl|NCBI__GCF_000009985.1:WP_011384888.1  641 REAVDFLRFYAAEARARFSQPVRLPgpvgesnelmlggRGVFACISPWNFPLAIFVGQVAAALAAGN 707 
                                                ********************9666699**************************************** PP

                                 TIGR01238  190 tviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlin 256 
                                                +v+akpa qt+l+aa av ll++aGvp+ ++ l+pG  + +G alt ++ +  ++ftGst++ar in
  lcl|NCBI__GCF_000009985.1:WP_011384888.1  708 AVVAKPAPQTPLMAAAAVRLLHQAGVPPQALHLVPGGPA-IGEALTVNPLVDAIAFTGSTATARHIN 773 
                                                ************************************666.*************************** PP

                                 TIGR01238  257 kalakredapvpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvl 323 
                                                +  a  + + +pliaetGG namivds+al+eqvvad l+saf saGqrcsalrv ++q++   r+ 
  lcl|NCBI__GCF_000009985.1:WP_011384888.1  774 RLRAAMDGPLAPLIAETGGLNAMIVDSSALPEQVVADCLESAFRSAGQRCSALRVAFIQREAWTRIQ 840 
                                                **99999999********************************************************* PP

                                 TIGR01238  324 tlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvap 390 
                                                 l+ Gam el +g p +l tdvGpvid+ ++++llah  ++++ ++ + q       +++ gtf ap
  lcl|NCBI__GCF_000009985.1:WP_011384888.1  841 PLLAGAMAELSLGDPALLSTDVGPVIDEASRRRLLAHGGRLRHAGRMIGQSACPP--DCRVGTFFAP 905 
                                                **************************************************99988..9********* PP

                                 TIGR01238  391 tlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGn 457 
                                                ++ +ld+ld l+ evfGp+lhv+ ++a +l++v+d + a+ ygltlG+hsri+ t++q+  ra++Gn
  lcl|NCBI__GCF_000009985.1:WP_011384888.1  906 MAHQLDNLDLLQSEVFGPILHVIPWEAGRLEQVLDCVAATSYGLTLGIHSRIDATIAQVIARARIGN 972 
                                                ******************************************************************* PP

                                 TIGR01238  458 vyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrl 495 
                                                +yvnr ++GavvG qpfGG GlsGtG kaGGp  l r+
  lcl|NCBI__GCF_000009985.1:WP_011384888.1  973 IYVNRTMIGAVVGSQPFGGLGLSGTGAKAGGPNTLIRY 1010
                                                ********************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1039 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 15.39
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources