Alignments for a candidate for argG in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Desulfacinum hydrothermale DSM 13146

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_084056568.1 B9A12_RS04100 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_900176285.1:WP_084056568.1
          Length = 403

 Score =  549 bits (1415), Expect = e-161
 Identities = 267/394 (67%), Positives = 318/394 (80%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61
           K+VLAYSGGLDTSIILKWL ETY+ +V+AF AD+GQGE++    EKAL+TGA KA   DL
Sbjct: 5   KVVLAYSGGLDTSIILKWLIETYQCQVVAFAADLGQGEDLSGIEEKALKTGAVKARVEDL 64

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           KEEFVRDFVFP  RA  +YEG YLLGTSIARPLIAK  V IA EEGA+A++HGATGKGND
Sbjct: 65  KEEFVRDFVFPAFRANVIYEGQYLLGTSIARPLIAKRQVEIAHEEGADAVSHGATGKGND 124

Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLHI 181
           QVRFELT   L P IKVIAPWREW  + R+ ++ +A  HGIPVPVT+EKPYS DANLLHI
Sbjct: 125 QVRFELTYMTLDPSIKVIAPWREWDLKSRQALMDFARHHGIPVPVTKEKPYSCDANLLHI 184

Query: 182 SYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQR 241
           SYEGG+LEDPW EP   MF +T DPE+APD PE +E+EF +GDPVAVNGE+LSPAALL R
Sbjct: 185 SYEGGILEDPWKEPDPSMFTLTVDPEKAPDKPETIEIEFQKGDPVAVNGEKLSPAALLAR 244

Query: 242 LNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDML 301
           LNEIGGRHGVGR D+VE+RFVGMKSRGVYETPGGTIL  A RA+ES+T+DREV+  RD L
Sbjct: 245 LNEIGGRHGVGRADVVESRFVGMKSRGVYETPGGTILRIAHRAMESITMDREVMFLRDSL 304

Query: 302 SPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQD 361
            P+YA+L+Y GFW+APER ALQ+  D   ++VTG  R+KL+KG+  V GRK+  SLY  +
Sbjct: 305 IPQYAKLIYNGFWFAPERVALQSLIDTSQQTVTGTVRVKLFKGHCMVTGRKSDLSLYDPE 364

Query: 362 LVSFDEAGGYDQKDAEGFIKIQALRLRVRALVER 395
           L +F+E   Y Q DA GFI++Q LRLR+++LV +
Sbjct: 365 LATFEEEDVYQQSDATGFIRLQGLRLRIQSLVRK 398


Lambda     K      H
   0.319    0.137    0.402 

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: 502
Number of extensions: 13
Number of successful extensions: 1
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: 400
Length of database: 403
Length adjustment: 31
Effective length of query: 369
Effective length of database: 372
Effective search space:   137268
Effective search space used:   137268
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_084056568.1 B9A12_RS04100 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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.aa/TIGR00032.hmm
# target sequence database:        /tmp/gapView.3673205.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-157  509.2   0.0   5.5e-157  509.0   0.0    1.0  1  NCBI__GCF_900176285.1:WP_084056568.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176285.1:WP_084056568.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  509.0   0.0  5.5e-157  5.5e-157       1     389 [.       5     393 ..       5     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 509.0 bits;  conditional E-value: 5.5e-157
                             TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaa 72 
                                           kvvlaysGGlDts++lk+l e   ++v+a+++d+Gq+ edl  ieekalk Ga+ka+v D +eefv+d++f+a
  NCBI__GCF_900176285.1:WP_084056568.1   5 KVVLAYSGGLDTSIILKWLIETyQCQVVAFAADLGQG-EDLSGIEEKALKTGAVKARVEDLKEEFVRDFVFPA 76 
                                           8*********************899***********9.9********************************** PP

                             TIGR00032  73 iqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvrele 145
                                            +an +yeg+Yll+t++aRpliak++ve+a++ega+av+hG+tgKGnDqvRFel+ ++l+p +kviaP+re++
  NCBI__GCF_900176285.1:WP_084056568.1  77 FRANVIYEGQYLLGTSIARPLIAKRQVEIAHEEGADAVSHGATGKGNDQVRFELTYMTLDPSIKVIAPWREWD 149
                                           ************************************************************************* PP

                             TIGR00032 146 li.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevvei 217
                                           l  R+ ++++a+++Gi+vpv+kek+ys D nll++s+E+g+LEdp+ ep   +++l++dp++++ d+pe++ei
  NCBI__GCF_900176285.1:WP_084056568.1 150 LKsRQALMDFARHHGIPVPVTKEKPYSCDANLLHISYEGGILEDPWKEPDPSMFTLTVDPEKAP-DKPETIEI 221
                                           *88*******************************************************999888.******** PP

                             TIGR00032 218 eFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvlt 290
                                           eF+kG Pva+nge+l+p  l+ ++nei+g+hGvGr D+vE R +g+KsR++YE+p+ ++L++Ah+++e+ +++
  NCBI__GCF_900176285.1:WP_084056568.1 222 EFQKGDPVAVNGEKLSPAALLARLNEIGGRHGVGRADVVESRFVGMKSRGVYETPGGTILRIAHRAMESITMD 294
                                           ************************************************************************* PP

                             TIGR00032 291 kdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvs 363
                                           ++v+ +++    +y++liY+G+wf p++ al++li+++q+ vtGtvrvklfkG+ +v grks+ slYd+el++
  NCBI__GCF_900176285.1:WP_084056568.1 295 REVMFLRDSLIPQYAKLIYNGFWFAPERVALQSLIDTSQQTVTGTVRVKLFKGHCMVTGRKSDLSLYDPELAT 367
                                           ************************************************************************* PP

                             TIGR00032 364 fekdkefdqkdaiGfikirglqikvy 389
                                           fe+++ ++q+da+Gfi+++gl+ ++ 
  NCBI__GCF_900176285.1:WP_084056568.1 368 FEEEDVYQQSDATGFIRLQGLRLRIQ 393
                                           *********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (403 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: 14.18
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis