Alignments for a candidate for argH in Pseudomonas stutzeri A1501

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Pseudomonas stutzeri A1501

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_011911754.1 PST_RS02680 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>NCBI__GCF_000013785.1:WP_011911754.1
          Length = 464

 Score =  448 bits (1152), Expect = e-130
 Identities = 231/453 (50%), Positives = 305/453 (67%), Gaps = 1/453 (0%)

Query: 5   QTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVAG 64
           Q+W  RF   +   +ARF AS+ FD  L  +D+ GS AHA MLA  G+++  E +Q++A 
Sbjct: 8   QSWGGRFSEPVDAFVARFTASVEFDKRLYRHDIMGSIAHATMLAKAGVLTDAERDQIIAN 67

Query: 65  LEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYLR 124
           L+ I+ E   G F   VD EDVH  +E RLT+ +G VGKKLHT RSRNDQV TD RL+LR
Sbjct: 68  LKDIQSEIEAGTFDWRVDLEDVHMNIEARLTDRIGIVGKKLHTGRSRNDQVATDIRLWLR 127

Query: 125 DQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWER 184
           D+I  I  E+   Q  LL +AE   +T++PG+THLQ AQPV+  HHLLA+F+M  RD+ER
Sbjct: 128 DEIDVILGEITRLQQGLLGLAEAEADTIMPGFTHLQTAQPVTFGHHLLAWFEMLSRDYER 187

Query: 185 LGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAA 244
           L D  +R N  PLG  ALAGTT+PI R  T +LL F+ I  NSLDGVSDRDFAIEF  AA
Sbjct: 188 LVDCRKRTNRMPLGSAALAGTTYPIQREITCELLGFEAISGNSLDGVSDRDFAIEFCAAA 247

Query: 245 SLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFGH 304
           S+ M+HLSR +EE++LW+S +F+F+ L D   TGSSIMPQKKNPDVPELVRGKTGRVFG 
Sbjct: 248 SVAMMHLSRFSEELVLWTSAQFQFIDLPDRFCTGSSIMPQKKNPDVPELVRGKTGRVFGA 307

Query: 305 LQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAVT 364
           L  +L +MKG PLAYNKD QEDKE LFD+ +T++ SL A   ++   ++ + + + +A  
Sbjct: 308 LTGLLALMKGQPLAYNKDNQEDKEPLFDAADTLRDSLRAFADMV-PAIKPKREIMREAAL 366

Query: 365 EDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAADI 424
             FS ATD+ADYL  +G+PFR+ + +VG  VK  +  GK L ++ L+E +Q       D+
Sbjct: 367 RGFSTATDLADYLVRKGLPFRDCHEIVGHAVKYGVQTGKDLAEMTLDELRQFSGEIGDDV 426

Query: 425 YEAISPRQVVAARNSHGGTGFVQVSKALIAARA 457
           +  ++    V AR+  GGT   QV  A+   +A
Sbjct: 427 FAVLTLEGSVNARDHIGGTAPAQVRAAVKRGQA 459


Lambda     K      H
   0.320    0.135    0.384 

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: 517
Number of extensions: 17
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: 461
Length of database: 464
Length adjustment: 33
Effective length of query: 428
Effective length of database: 431
Effective search space:   184468
Effective search space used:   184468
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: 51 (24.3 bits)

Align candidate WP_011911754.1 PST_RS02680 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

# 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/TIGR00838.hmm
# target sequence database:        /tmp/gapView.25321.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00838  [M=455]
Accession:   TIGR00838
Description: argH: argininosuccinate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-197  643.1   0.0   1.6e-197  642.9   0.0    1.0  1  lcl|NCBI__GCF_000013785.1:WP_011911754.1  PST_RS02680 argininosuccinate ly


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013785.1:WP_011911754.1  PST_RS02680 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  642.9   0.0  1.6e-197  1.6e-197       2     452 ..      10     459 ..       9     462 .. 0.99

  Alignments for each domain:
  == domain 1  score: 642.9 bits;  conditional E-value: 1.6e-197
                                 TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg 70 
                                               wggR+++ +d  va+f+as++fDk+l+++Di gsiah+++Lakag+lt+ e++++i++L+++++e+++g
  lcl|NCBI__GCF_000013785.1:WP_011911754.1  10 WGGRFSEPVDAFVARFTASVEFDKRLYRHDIMGSIAHATMLAKAGVLTDAERDQIIANLKDIQSEIEAG 78 
                                               9******************************************************************** PP

                                 TIGR00838  71 klelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalve 139
                                               +++++vd eD+H+++E++l+d++g  vgkklhtgrsRnDqvatd+rl+lrd+++ ++ ++  l++ l+ 
  lcl|NCBI__GCF_000013785.1:WP_011911754.1  79 TFDWRVDLEDVHMNIEARLTDRIG-IVGKKLHTGRSRNDQVATDIRLWLRDEIDVILGEITRLQQGLLG 146
                                               ************************.9******************************************* PP

                                 TIGR00838 140 kAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidre 208
                                               +Ae+e +t+mpg+tHLq AqP+t++Hhlla++eml+rD+eRl+d  kR+n+ PlGs+Alagt+++i+re
  lcl|NCBI__GCF_000013785.1:WP_011911754.1 147 LAEAEADTIMPGFTHLQTAQPVTFGHHLLAWFEMLSRDYERLVDCRKRTNRMPLGSAALAGTTYPIQRE 215
                                               ********************************************************************* PP

                                 TIGR00838 209 llaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssi 277
                                                + elLgF+a+  nsld+vsdRDf+iE+ +aa+++m+hlsr++Eel+l++s+ f+f++l+d++++gssi
  lcl|NCBI__GCF_000013785.1:WP_011911754.1 216 ITCELLGFEAISGNSLDGVSDRDFAIEFCAAASVAMMHLSRFSEELVLWTSAQFQFIDLPDRFCTGSSI 284
                                               ********************************************************************* PP

                                 TIGR00838 278 mPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllke 346
                                               mPqKKnpDv El+Rgktgrv+G ltgll+++K++PlaYnkD qEdke+lfda +t++++l++++ ++  
  lcl|NCBI__GCF_000013785.1:WP_011911754.1 285 MPQKKNPDVPELVRGKTGRVFGALTGLLALMKGQPLAYNKDNQEDKEPLFDAADTLRDSLRAFADMVPA 353
                                               ********************************************************************* PP

                                 TIGR00838 347 lkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekl 415
                                               +k ++e ++eaa ++f++atdlAdylvrkG+PFR+ heivG++v++ +++Gk+l e+tl+el+++s ++
  lcl|NCBI__GCF_000013785.1:WP_011911754.1 354 IKPKREIMREAALRGFSTATDLADYLVRKGLPFRDCHEIVGHAVKYGVQTGKDLAEMTLDELRQFSGEI 422
                                               ********************************************************************* PP

                                 TIGR00838 416 eedvlevldleeavekrdakGGtakeevekaieeaka 452
                                                +dv+ vl+le +v++rd +GGta+++v+ a++  +a
  lcl|NCBI__GCF_000013785.1:WP_011911754.1 423 GDDVFAVLTLEGSVNARDHIGGTAPAQVRAAVKRGQA 459
                                               *******************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (464 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: 00:00:00.02
# Mc/sec: 8.82
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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