Alignments for a candidate for putA in Desulfacinum hydrothermale DSM 13146

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Desulfacinum hydrothermale DSM 13146

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_084058850.1 B9A12_RS14640 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_900176285.1:WP_084058850.1
          Length = 994

 Score =  516 bits (1330), Expect = e-150
 Identities = 256/510 (50%), Positives = 348/510 (68%)

Query: 4   PYKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKDQL 63
           P+++EP  D+T+   R+AFE+ L  + KE   + PL+IN ++V T++   S NP R DQ+
Sbjct: 473 PFENEPPWDWTLAEVRQAFEKTLRKLPKEFPVKVPLVINDKKVQTQETFSSTNPNRTDQV 532

Query: 64  VGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEA 123
           VG V+ A +  A +A+ +A EAF  WR+  P ERA  L +AA   R R++E +A  V+E 
Sbjct: 533 VGVVASAGEKKAREAVAAAKEAFAAWRDTPPRERAEYLFRAAQAARSRRYELAALQVYEV 592

Query: 124 GKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNF 183
           GK WKEAD D  EAIDFLEYY R+MI L   + + + PGE +  FY P GV   ++PWNF
Sbjct: 593 GKSWKEADGDVCEAIDFLEYYGREMIRLGAPRRMGNVPGEVSHLFYEPRGVAAVVAPWNF 652

Query: 184 ALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGD 243
             AI VG   A +VTGNTVV KPAS +PV+      + ++A LPKGV+N++PG GA++GD
Sbjct: 653 PFAISVGMTSAALVTGNTVVYKPASQSPVIGYWLYRIFQEAKLPKGVLNFLPGPGAKIGD 712

Query: 244 YLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDL 303
           +LV HP  ++I FTGSK+VG+R+ ERAA   P  + +K V+ EMGGK+ +++D DADLD 
Sbjct: 713 FLVTHPDVAMIAFTGSKEVGLRIIERAAKTPPDAHFVKNVVAEMGGKNAIIIDADADLDE 772

Query: 304 AAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVI 363
           A   +L SAFG+ GQKCSA SR ++ ++ Y ++LE+  A A++L +G   +  N MG VI
Sbjct: 773 AVVHVLHSAFGYQGQKCSACSRLIVLEENYHKLLERLRAAAESLELGPVEDAKNVMGAVI 832

Query: 364 DEKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVA 423
           D KA EKI+ YIEIGK+EG+++     + S G+F+  TI  D+ PE  + QEEIFGPV++
Sbjct: 833 DAKAREKILEYIEIGKREGKVLVERPVEGSNGYFVPLTIFTDIRPEHRLAQEEIFGPVLS 892

Query: 424 FSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHP 483
             K  DFD ALE+AN+T+Y LTGAV +R+  +IE+A+R F VGNLY NR  TGAIV  HP
Sbjct: 893 VMKVRDFDEALEVANSTQYALTGAVFSRSPENIEKARRRFRVGNLYINRGSTGAIVERHP 952

Query: 484 FGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513
           FGGFKMSG  SKAGGPDYL   M  + V+E
Sbjct: 953 FGGFKMSGVGSKAGGPDYLLQFMVPRNVAE 982


Lambda     K      H
   0.316    0.134    0.388 

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: 1221
Number of extensions: 40
Number of successful extensions: 2
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: 515
Length of database: 994
Length adjustment: 39
Effective length of query: 476
Effective length of database: 955
Effective search space:   454580
Effective search space used:   454580
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: 55 (25.8 bits)

Align candidate WP_084058850.1 B9A12_RS14640 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01237 (pruA: putative 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/TIGR01237.hmm
# target sequence database:        /tmp/gapView.552271.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01237  [M=511]
Accession:   TIGR01237
Description: D1pyr5carbox2: putative 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-205  669.8   0.0   1.8e-205  669.5   0.0    1.1  1  NCBI__GCF_900176285.1:WP_084058850.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176285.1:WP_084058850.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  669.5   0.0  1.8e-205  1.8e-205       2     510 ..     475     983 ..     474     984 .. 0.99

  Alignments for each domain:
  == domain 1  score: 669.5 bits;  conditional E-value: 1.8e-205
                             TIGR01237   2 knepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasvedaeqa 74 
                                           +nep  d++ +e +qaf+k+l k+ + +  + plvin ++v+t++  +s np ++++vvG va a  ++a +a
  NCBI__GCF_900176285.1:WP_084058850.1 475 ENEPPWDWTLAEVRQAFEKTLRKLPKEFPVKVPLVINDKKVQTQETFSSTNPNRTDQVVGVVASAGEKKAREA 547
                                           789999******************9999999****************************************** PP

                             TIGR01237  75 lqaakkafeewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyyaremikl 147
                                           + aak+af +w+ t+++era+ l++aa+  + rr+el+al v evGk+++ead +v+eaidfleyy remi+l
  NCBI__GCF_900176285.1:WP_084058850.1 548 VAAAKEAFAAWRDTPPRERAEYLFRAAQAARSRRYELAALQVYEVGKSWKEADGDVCEAIDFLEYYGREMIRL 620
                                           ************************************************************************* PP

                             TIGR01237 148 akskevlsieGeknrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatviaaklveileea 220
                                              +   +++Ge  +++y p+Gva v++pwnfp+ai vGmt a++vtGn+vv kpa++++vi   l  i++ea
  NCBI__GCF_900176285.1:WP_084058850.1 621 GAPRRMGNVPGEVSHLFYEPRGVAAVVAPWNFPFAISVGMTSAALVTGNTVVYKPASQSPVIGYWLYRIFQEA 693
                                           ************************************************************************* PP

                             TIGR01237 221 GlpkGvlqfvpGkGsevGeylvdhpktrlitftGsrevGlriyedaakvqpGqkhlkrviaelGGkdavivde 293
                                            lpkGvl+f+pG G ++G++lv+hp++ +i+ftGs+evGlri e+aak  p  +++k v+ae+GGk+a+i+d 
  NCBI__GCF_900176285.1:WP_084058850.1 694 KLPKGVLNFLPGPGAKIGDFLVTHPDVAMIAFTGSKEVGLRIIERAAKTPPDAHFVKNVVAEMGGKNAIIIDA 766
                                           ************************************************************************* PP

                             TIGR01237 294 sadieqavaaavtsafGfaGqkcsaasrvvvlekvydevverfveatkslkvgktdeadvqvgpvidqksfdk 366
                                           +ad+++av  +++safG++Gqkcsa+sr++vle+ y +++er+  a++sl++g+ ++a+  +g+vid+k+ +k
  NCBI__GCF_900176285.1:WP_084058850.1 767 DADLDEAVVHVLHSAFGYQGQKCSACSRLIVLEENYHKLLERLRAAAESLELGPVEDAKNVMGAVIDAKAREK 839
                                           ************************************************************************* PP

                             TIGR01237 367 ikeyielgkaegklvlggedddskGyfikptifkdvdrkarlaqeeifGpvvavlrakdfdealeiansteyg 439
                                           i eyie+gk egk+++    ++s+Gyf+  tif+d+ ++ rlaqeeifGpv++v++++dfdeale+anst+y+
  NCBI__GCF_900176285.1:WP_084058850.1 840 ILEYIEIGKREGKVLVERPVEGSNGYFVPLTIFTDIRPEHRLAQEEIFGPVLSVMKVRDFDEALEVANSTQYA 912
                                           ************************************************************************* PP

                             TIGR01237 440 ltGgvisnsrerierakaefevGnlyfnrkitGaivgvqpfGGfkmsGtdskaGGpdylaqflqaktvter 510
                                           ltG+v+s+s+e+ie+a+  f+vGnly+nr  tGaiv ++pfGGfkmsG++skaGGpdyl+qf+ +++v+e+
  NCBI__GCF_900176285.1:WP_084058850.1 913 LTGAVFSRSPENIEKARRRFRVGNLYINRGSTGAIVERHPFGGFKMSGVGSKAGGPDYLLQFMVPRNVAEN 983
                                           *********************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (994 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: 32.74
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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