Alignments for a candidate for rocA in Sphingopyxis indica DS15

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Sphingopyxis indica DS15

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_089216122.1 CHB69_RS10610 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::ANA3:7023590
         (1064 letters)



>NCBI__GCF_900188185.1:WP_089216122.1
          Length = 1030

 Score =  907 bits (2345), Expect = 0.0
 Identities = 498/1030 (48%), Positives = 677/1030 (65%), Gaps = 26/1030 (2%)

Query: 37   EEQYLSELIKLVPSSDEAIERVTRRAHELVNKVRQFDKKGLMVGIDAFLQQYSLETQEGI 96
            E   +++L   +  S    E VT R   L+ K +   ++  +V     + +Y L T+EG+
Sbjct: 18   EADIVADLRTALARSPATAEAVTARGLTLIRKAKAEGERETLVA--QLMNRYRLSTEEGV 75

Query: 97   ILMCLAEALLRIPDAATADALIEDKLSGAKWDEHLSKSDSVLVNASTWGLMLTGKIVKLD 156
            +LMCLAEALLR+PD ATA+ALI DK++G  W E   +   ++V  S  GL L    + LD
Sbjct: 76   VLMCLAEALLRVPDNATANALIRDKIAGRHWAEGDDEDSPLVVALSARGLSLGSATLMLD 135

Query: 157  KK-IDGTPSNLLSRLVNRLGEPVIRQAMMAAMKIMGKQFVLGRTMKEALKNSE-DKRKLG 214
                   P  +L  ++ R GEPVIRQA +AAMK++G+QFV+G ++  A++ ++ DK +L 
Sbjct: 136  AMGSQAKPLAILRTMIRRSGEPVIRQAALAAMKLLGQQFVMGESIDAAVRRADKDKSELA 195

Query: 215  YTHSYDMLGEAALTRKDAEKYFNDYANAITELGAQSYNENESPRPTISIKLSALHPRYEV 274
               S+DMLGEAA T  DA +Y++ YA AI  +G  +   +      ISIKLSALHPRYE 
Sbjct: 196  ---SFDMLGEAARTAADARRYYDSYAAAIARIGRDAKPGDPFANHGISIKLSALHPRYEY 252

Query: 275  ANEDRVLTELYDTVIRLIKLARGLNIGISIDAEEVDRLELSLKLFQKLFNADATKGWGLL 334
                RV  EL   VI L   AR +NI + IDAEE DRLE  L ++  L +A    GW  L
Sbjct: 253  LQGQRVRDELIPRVIELAVAARRVNIPLMIDAEESDRLEPHLDVYGALIDAGIADGWTGL 312

Query: 335  GIVVQAYSKRALPVLVWLTRLAKEQGDEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRK 394
            GIVVQAY KRA  V+ W+   A+ +G  + +RLVKGAYWD+E+K AQ  G   +P++T K
Sbjct: 313  GIVVQAYQKRASEVIRWVAARARRRGVMLSMRLVKGAYWDTEIKRAQTLGLGDFPVFTAK 372

Query: 395  AGTDVSYLACARYLLSDATRGAIYPQFASHNAQTVAAISDMAGDRNHEFQRLHGMGQELY 454
              TD++YLACA+ L     +  I+P FASHNA T+A ++++    ++E QRLHGMG+  +
Sbjct: 373  LHTDLNYLACAQILRE--CQDCIFPAFASHNAMTLAFVTELFAGADYELQRLHGMGEGAH 430

Query: 455  DTILS-EAGAKAVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLVVHP 513
            D I++     + VR+YAP+G H+DLL YLVRRLLENGAN+SFVH+  DP    E L V P
Sbjct: 431  DAIVALSPPPRPVRVYAPVGTHRDLLAYLVRRLLENGANSSFVHQFSDPDVSAEELAVDP 490

Query: 514  LKTLTGYKTLANNKIVLPT--DIFGSDRKNSKGLNMNIISEAEPFFAALDKFKSTQWQAG 571
                   +++A+    LPT   ++   R+NS+G ++      E   AA+ + +     A 
Sbjct: 491  -------RSVASAPSKLPTGLQLYDPVRRNSRGYDLGEPGVPEALIAAIAEARDAGAVAA 543

Query: 572  PLVNGQTLTGEHKTVVSPFDTTQTVGQVAFADKAAIEQAVASADAAFATWTRTPVEVRAS 631
            P+V G+   G+ + V +P  T   +G+V  AD AA+E+AVA+A  A   W+      RA 
Sbjct: 544  PIVGGRERRGKGEPVHNPA-TGVVIGRVVEADAAAVEEAVAAARKAQGDWSLAGGAFRAE 602

Query: 632  ALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMSKPELLP 691
             L++ ADL+EE     + L   EAGK++ D + EVREAVDF RYYA QA+   S P  LP
Sbjct: 603  RLERAADLIEERDALFLGLAMDEAGKTLVDAVAEVREAVDFLRYYAAQARADFSWPVTLP 662

Query: 692  GPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIGYRAV 751
            GPTGE NEL L+G+G+F CISPWNFPLAIFLGQVSAALAAGN V+AKPAEQT +I + AV
Sbjct: 663  GPTGERNELILEGKGIFACISPWNFPLAIFLGQVSAALAAGNAVLAKPAEQTPLIAHAAV 722

Query: 752  QLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLANREGAII 811
            +   +AG+P D+L YLPG G TVG ALT  + + GV FTGST  A+ INR+LA REG I 
Sbjct: 723  ETLLEAGVPGDILHYLPGRGETVGAALTGHDDVIGVAFTGSTEVARAINRSLAMREGPIA 782

Query: 812  PLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQ 871
             LIAETGG NAM+VDST+ PEQV  D V+S+F SAGQRCSALR+L +Q+D+AD +I ++ 
Sbjct: 783  TLIAETGGANAMIVDSTALPEQVARDAVASAFQSAGQRCSALRLLCVQDDVADAMIAMVA 842

Query: 872  GAMDELVIGNPSSVKTDVGPVIDATAKANLDAHIDHIKQVGKLIKQMS---LPAGTENGH 928
            GAM EL +G+P+ + TDVGP+ID  A++N+ A+++  +  G+LI + +   LPAG   G 
Sbjct: 843  GAMAELNVGDPAILATDVGPIIDEEAQSNIAAYVEEARAAGRLIAEAARTKLPAG---GT 899

Query: 929  FVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSRNEGHA 988
            FV+P  + +D +  L++E FGP+LHV  +K  EL  +ID IN++G+GLTLG+H+R +  A
Sbjct: 900  FVAPAMIRLDHVTDLKREIFGPVLHVATWKGGELDALIDAINASGYGLTLGVHTRIDSVA 959

Query: 989  LEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNIT 1048
              VA +  VGNVY+NRNQIGA+VG QPFGG+GLSGTGPKAGGP+YL RF  EK+ + +IT
Sbjct: 960  AHVAARAQVGNVYVNRNQIGAIVGSQPFGGRGLSGTGPKAGGPNYLRRFAEEKSISTDIT 1019

Query: 1049 AIGGNATLLS 1058
            A GGNA L++
Sbjct: 1020 AAGGNAALMA 1029


Lambda     K      H
   0.317    0.133    0.377 

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: 2394
Number of extensions: 98
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1064
Length of database: 1030
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 985
Effective search space:  1003715
Effective search space used:  1003715
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)

Align candidate WP_089216122.1 CHB69_RS10610 (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.179970.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.9e-196  637.5   6.0   9.5e-196  637.0   6.0    1.2  1  NCBI__GCF_900188185.1:WP_089216122.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188185.1:WP_089216122.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  637.0   6.0  9.5e-196  9.5e-196       2     497 ..     506    1010 ..     505    1013 .. 0.98

  Alignments for each domain:
  == domain 1  score: 637.0 bits;  conditional E-value: 9.5e-196
                             TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsead 72  
                                            ly   r+ns G dl    + + l + + +a +    aapivg++ +  g+ +pv npa    ++G+v ead
  NCBI__GCF_900188185.1:WP_089216122.1  506 LYDPVRRNSRGYDLGEPGVPEALIAAIAEARDAGAVAAPIVGGRER-RGKGEPVHNPAT-GVVIGRVVEAD 574 
                                            89999************************************87655.68899*****96.6899******* PP

                             TIGR01238   73 aaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflr 143 
                                            aa v+eav +a +a   ws    + ra  ler+adl+e++   +++l++ eaGktl +a+aevreavdflr
  NCBI__GCF_900188185.1:WP_089216122.1  575 AAAVEEAVAAARKAQGDWSLAGGAFRAERLERAADLIEERDALFLGLAMDEAGKTLVDAVAEVREAVDFLR 645 
                                            *********************************************************************** PP

                             TIGR01238  144 yyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsl 201 
                                            yya q++ +++   + +             +G + cispwnfplaif+Gq++aalaaGn+v+akpaeqt+l
  NCBI__GCF_900188185.1:WP_089216122.1  646 YYAAQARADFSWPVTLPgptgernelilegKGIFACISPWNFPLAIFLGQVSAALAAGNAVLAKPAEQTPL 716 
                                            **********9987777899999************************************************ PP

                             TIGR01238  202 iaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliae 272 
                                            ia  ave l+eaGvp  ++  lpGrGe+vGaalt ++ + Gv+ftGstevar in++la re + ++liae
  NCBI__GCF_900188185.1:WP_089216122.1  717 IAHAAVETLLEAGVPGDILHYLPGRGETVGAALTGHDDVIGVAFTGSTEVARAINRSLAMREGPIATLIAE 787 
                                            *********************************************************************** PP

                             TIGR01238  273 tGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirltt 343 
                                            tGG namivdstal+eqv +d +asaf+saGqrcsalr+lcvq+dvad ++ ++ Gam el+vg p  l t
  NCBI__GCF_900188185.1:WP_089216122.1  788 TGGANAMIVDSTALPEQVARDAVASAFQSAGQRCSALRLLCVQDDVADAMIAMVAGAMAELNVGDPAILAT 858 
                                            *********************************************************************** PP

                             TIGR01238  344 dvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvr 414 
                                            dvGp+id+ea+ n+ a++e+ +a ++ +a++ + +      gtfvap ++ ld++ +lk+e+fGpvlhv  
  NCBI__GCF_900188185.1:WP_089216122.1  859 DVGPIIDEEAQSNIAAYVEEARAAGRLIAEAARTK--LPAGGTFVAPAMIRLDHVTDLKREIFGPVLHVAT 927 
                                            *******************************9998..7789****************************** PP

                             TIGR01238  415 ykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpk 485 
                                            +k  eld ++d ina+GygltlGvh+ri++  +++  ra+vGnvyvnrn++Ga+vG qpfGG+GlsGtGpk
  NCBI__GCF_900188185.1:WP_089216122.1  928 WKGGELDALIDAINASGYGLTLGVHTRIDSVAAHVAARAQVGNVYVNRNQIGAIVGSQPFGGRGLSGTGPK 998 
                                            *********************************************************************** PP

                             TIGR01238  486 aGGplylyrltr 497 
                                            aGGp yl r+ +
  NCBI__GCF_900188185.1:WP_089216122.1  999 AGGPNYLRRFAE 1010
                                            *********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1030 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 33.59
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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