Alignments for a candidate for putA in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Herbaspirillum autotrophicum IAM 14942

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_050461642.1 AKL27_RS04800 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

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



>NCBI__GCF_001189915.1:WP_050461642.1
          Length = 1218

 Score = 1847 bits (4785), Expect = 0.0
 Identities = 956/1230 (77%), Positives = 1030/1230 (83%), Gaps = 12/1230 (0%)

Query: 1    MTHVASAAVAAPFGGFQAELLPTPSPLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDAT 60
            MT  +  + +  F  FQ  LLP P+PL+AAIT+ YRRDE  AVQWLL Q+Q    W DAT
Sbjct: 1    MTATSQISPSPAFEAFQQALLPAPTPLQAAITSVYRRDETAAVQWLLTQIQSNDQWTDAT 60

Query: 61   QQLARKLVQQVREKRTRSSGVDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIAD 120
              LA  LVQ VR KRTR+SGVDALMHEFSLSSEEGVALMCLAEALLRIPD QTADRLIAD
Sbjct: 61   HTLAHTLVQAVRTKRTRASGVDALMHEFSLSSEEGVALMCLAEALLRIPDHQTADRLIAD 120

Query: 121  KISKGDWRKHLGESPSLFVNAATWGLLITGKLVSTSSESGLTQAITRLIGKGGEPLIRKG 180
            KISKGDWR+HLGESPSLFVNAATWGLLITGKLVST+SE+ LT A+TRLI KGGEPLIRKG
Sbjct: 121  KISKGDWRRHLGESPSLFVNAATWGLLITGKLVSTNSENSLTSALTRLINKGGEPLIRKG 180

Query: 181  VDLAMRMLGNQFVTGQTIEEALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESA 240
            VDLAMRMLGNQFVTGQTI EAL NSRENEKRGYRYSYDMLGEAALT HDAD YY+ YE A
Sbjct: 181  VDLAMRMLGNQFVTGQTIAEALSNSRENEKRGYRYSYDMLGEAALTGHDADYYYRCYEEA 240

Query: 241  IHAIGRASNGRGIKDGPGISVKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGL 300
            IHAIGRASNGRGIKDGPGISVKLSALHPRYSRAQHARVM ELLPRLKQLL+LAK Y+IGL
Sbjct: 241  IHAIGRASNGRGIKDGPGISVKLSALHPRYSRAQHARVMGELLPRLKQLLVLAKSYNIGL 300

Query: 301  NIDAEEADRLELSLDMMEVLVADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRR 360
            NIDAEEADRLELSL++MEVL  DPDL GF+G+GFVVQ YQKRCPFVIDYLVDLARR+GR+
Sbjct: 301  NIDAEEADRLELSLNLMEVLAFDPDLDGFEGIGFVVQAYQKRCPFVIDYLVDLARRSGRK 360

Query: 361  LMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVHTDLSYLTCAQKLLAATDVIYPQFATH 420
            LM+RLVKGAYWDSEIKRAQVDGL GYPVYTRKVHTDLSYL CAQKLLA+T VIYPQFATH
Sbjct: 361  LMVRLVKGAYWDSEIKRAQVDGLSGYPVYTRKVHTDLSYLVCAQKLLASTAVIYPQFATH 420

Query: 421  NAHTLAAIYHWARQHQIDNYEFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLA 480
            NAHTLAAIY WA+QHQI +YEFQCLHGMGETLYDQVVG D LGKACR+YAPVGSHQTLLA
Sbjct: 421  NAHTLAAIYTWAQQHQITDYEFQCLHGMGETLYDQVVGDDKLGKACRIYAPVGSHQTLLA 480

Query: 481  YLVRRLLENGANSSFVNQIVDEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERK 540
            YLVRRLLENGANSSFVNQIVDEAV +D L+ DP+E VR  GG  H  I +P  LYGEERK
Sbjct: 481  YLVRRLLENGANSSFVNQIVDEAVAIDTLIADPVEAVRQTGGAAHAQIPLPRDLYGEERK 540

Query: 541  NSAGIDLSNEDRLQQLGQLFISMADRQWQAAPLLAADTAAQSAQAAQLVRNPADLREVVG 600
            NS GIDLSNED L+ LG+ F  +A  +WQA PLL     A        + NPAD R+ VG
Sbjct: 541  NSGGIDLSNEDSLRDLGREFAQLAGHEWQAGPLLQGRVTATPDLD---ILNPADHRDRVG 597

Query: 601  QVSEATVADVDTALRAATDYAPQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGK 660
            +V+EA   DV+TAL AATDYAPQWQ+ PATERA MLERAADLLE+H  ELMALAVREAGK
Sbjct: 598  RVAEANGDDVETALAAATDYAPQWQALPATERAQMLERAADLLEQHRVELMALAVREAGK 657

Query: 661  SLPNAIAEVREAVDFLRYYAIASRHDGNVLAWGPVVCISPWNFPLAIFIGEVSAALAAGN 720
            SLPNAIAEVREAVDFLRYYA+ S+ DGNVLAWGPVVCISPWNFPLAIF+GE+SAALAAGN
Sbjct: 658  SLPNAIAEVREAVDFLRYYAVQSQRDGNVLAWGPVVCISPWNFPLAIFVGEISAALAAGN 717

Query: 721  VVLAKPAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGST 780
            VVLAKPAEQT LIAHRAVQLLH AGIP AALQ LPGRGETVGA LTSD RVKGVIFTGST
Sbjct: 718  VVLAKPAEQTPLIAHRAVQLLHAAGIPLAALQFLPGRGETVGARLTSDERVKGVIFTGST 777

Query: 781  EVAQLINRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFD 840
            EVAQLINRTLA+R  D      EHG++PLIAETGGQNALIVDSSAL EQVVQDVLSSAFD
Sbjct: 778  EVAQLINRTLAKRVKD------EHGDLPLIAETGGQNALIVDSSALPEQVVQDVLSSAFD 831

Query: 841  SAGQRCSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDH 900
            SAGQRCSALR+LCLQ DIAD+T+ MLKGAM ELR+GRPDRL  DIGPVIDAEAR  LL H
Sbjct: 832  SAGQRCSALRVLCLQHDIADKTMTMLKGAMEELRIGRPDRLVTDIGPVIDAEARDQLLAH 891

Query: 901  IERMRASARAVHQLPLGEECQHGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQ 960
            IE+MR     V+QLPL E+  +GTFV PTVIEID LAQLQREVFGPVLHVLRYRRD LPQ
Sbjct: 892  IEQMRGQGCKVYQLPLDEQTGYGTFVPPTVIEIDSLAQLQREVFGPVLHVLRYRRDELPQ 951

Query: 961  LIDAINATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGT 1020
            LIDAINATGYGLTLGVHSRIDETI FVA RAHVGNIYVNRNIVGAVVGVQPFGGEGKSGT
Sbjct: 952  LIDAINATGYGLTLGVHSRIDETINFVAGRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGT 1011

Query: 1021 GPKAGGPLYLKRLQRNAQLHEELTRAQPADVPNALLDSLLDWARTHGHERLAANGQRYHR 1080
            GPKAGGPLYLKRLQR  Q    LT       P+  L  LL+WA THGH +LA  G  Y  
Sbjct: 1012 GPKAGGPLYLKRLQRQPQ---PLTPTVAEAAPSTTLAVLLEWAATHGHAKLATLGNSYVA 1068

Query: 1081 DSLLQRSLVLPGPTGERNTLGFAPRGLVLCAAGSVGTLLNQLAAAFATGNTALVDERSAA 1140
            +SLL  +L LPGPTGERNTL FA RG +LC A SV  LLNQLAA  ATGNTA+VD  +A 
Sbjct: 1069 ESLLDTTLALPGPTGERNTLSFAARGKMLCIATSVPALLNQLAAVLATGNTAVVDAATAQ 1128

Query: 1141 ILPSGLPAPVRAAIRRASQLDAEPLQAALVDSHQAAHWRARLAAREGALVPLILCGEDTT 1200
             LP+GLP  VR  +  + Q     L  ALVD+     WRA+LAAR+GALVPLI+  +D  
Sbjct: 1129 YLPAGLPEMVRQQVIVSDQPGTLALHLALVDAPACVQWRAQLAARDGALVPLIVTTDDAP 1188

Query: 1201 IPLWRLLAERALCINTTAAGGNASLMTISV 1230
            I LWRL+AERALCINTTAAGGNASLMT+ V
Sbjct: 1189 IALWRLVAERALCINTTAAGGNASLMTLEV 1218


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: 3797
Number of extensions: 143
Number of successful extensions: 5
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: 1230
Length of database: 1218
Length adjustment: 47
Effective length of query: 1183
Effective length of database: 1171
Effective search space:  1385293
Effective search space used:  1385293
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: 59 (27.3 bits)

Align candidate WP_050461642.1 AKL27_RS04800 (trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase)
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.686714.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-235  766.7   1.5   5.6e-235  766.4   0.1    1.8  2  NCBI__GCF_001189915.1:WP_050461642.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001189915.1:WP_050461642.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  766.4   0.1  5.6e-235  5.6e-235       1     498 [.     533    1027 ..     533    1029 .. 0.98
   2 ?   -1.8   0.2     0.045     0.045     159     197 ..    1091    1126 ..    1085    1135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 766.4 bits;  conditional E-value: 5.6e-235
                             TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71  
                                            dlyge rkns G+dl+ne+ l++l  ++ + a +++qa p+++++  a  + + + npad++d vG+v ea
  NCBI__GCF_001189915.1:WP_050461642.1  533 DLYGEERKNSGGIDLSNEDSLRDLGREFAQLAGHEWQAGPLLQGRVTATPDLD-ILNPADHRDRVGRVAEA 602 
                                            89****************************************99999988876.99*************** PP

                             TIGR01238   72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdfl 142 
                                            + ++v+ a+ +a + +++w+a++a era +ler+adlle+h  el+al+vreaGk+l naiaevreavdfl
  NCBI__GCF_001189915.1:WP_050461642.1  603 NGDDVETALAAATDYAPQWQALPATERAQMLERAADLLEQHRVELMALAVREAGKSLPNAIAEVREAVDFL 673 
                                            *********************************************************************** PP

                             TIGR01238  143 ryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqea 213 
                                            ryya q +    + ++ a G+vvcispwnfplaif+G+i+aalaaGn v+akpaeqt+lia rav+ll+ a
  NCBI__GCF_001189915.1:WP_050461642.1  674 RYYAVQSQR---DGNVLAWGPVVCISPWNFPLAIFVGEISAALAAGNVVLAKPAEQTPLIAHRAVQLLHAA 741 
                                            ****99943...344789***************************************************** PP

                             TIGR01238  214 GvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamiv 281 
                                            G+p +++q+lpGrGe+vGa ltsder++GviftGsteva+lin++lakr +++    pliaetGGqna+iv
  NCBI__GCF_001189915.1:WP_050461642.1  742 GIPLAALQFLPGRGETVGARLTSDERVKGVIFTGSTEVAQLINRTLAKRVKDEhgdLPLIAETGGQNALIV 812 
                                            *************************************************87766779************** PP

                             TIGR01238  282 dstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidae 352 
                                            ds+al+eqvv+dvl+safdsaGqrcsalrvlc+q+d+ad+++t++kGam+el++g+p rl td+Gpvidae
  NCBI__GCF_001189915.1:WP_050461642.1  813 DSSALPEQVVQDVLSSAFDSAGQRCSALRVLCLQHDIADKTMTMLKGAMEELRIGRPDRLVTDIGPVIDAE 883 
                                            *********************************************************************** PP

                             TIGR01238  353 akqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkv 423 
                                            a+++llahie+m++++ kv+q+ l++  ++  gtfv+pt++e+d+l++l++evfGpvlhv+ry++del ++
  NCBI__GCF_001189915.1:WP_050461642.1  884 ARDQLLAHIEQMRGQGCKVYQLPLDE--QTGYGTFVPPTVIEIDSLAQLQREVFGPVLHVLRYRRDELPQL 952 
                                            *************************9..8999*************************************** PP

                             TIGR01238  424 vdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyr 494 
                                            +d ina+GygltlGvhsri+et++++ +ra+vGn+yvnrn+vGavvGvqpfGGeG sGtGpkaGGplyl+r
  NCBI__GCF_001189915.1:WP_050461642.1  953 IDAINATGYGLTLGVHSRIDETINFVAGRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGTGPKAGGPLYLKR 1023
                                            *********************************************************************** PP

                             TIGR01238  495 ltrv 498 
                                            l r 
  NCBI__GCF_001189915.1:WP_050461642.1 1024 LQRQ 1027
                                            9875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.045
                             TIGR01238  159 kalGavvcispwnfplaiftGqiaaalaaGntviakpae 197 
                                             a+G ++ci+     +  ++ q+aa la+Gnt +   a 
  NCBI__GCF_001189915.1:WP_050461642.1 1091 AARGKMLCIATS---VPALLNQLAAVLATGNTAVVDAAT 1126
                                            567777787653...3456899**********9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1218 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 38.42
//
[ok]

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

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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