Alignments for a candidate for arcA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcA in Pseudomonas stutzeri RCH2

Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate GFF271 Psest_0272 arginine deiminase

Query= BRENDA::P13981
         (418 letters)



>FitnessBrowser__psRCH2:GFF271
          Length = 417

 Score =  701 bits (1809), Expect = 0.0
 Identities = 331/415 (79%), Positives = 376/415 (90%)

Query: 4   EKTKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMR 63
           +  KLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDV+WV+QAKRDHFDFV+KMR
Sbjct: 3   QSPKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVLWVSQAKRDHFDFVSKMR 62

Query: 64  ERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYL 123
           ERG++VLEMHNLLTET+ +PEALKW+LDRKITA+ VGLGL  E+RSWLE LE R+LAE+L
Sbjct: 63  ERGVEVLEMHNLLTETLSDPEALKWLLDRKITANQVGLGLQGEVRSWLEGLERRQLAEFL 122

Query: 124 IGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWP 183
           IGGV+  DLP SEG  I++M+R+YLGHSSF+LPPLPNT FTRDTTCWIYGGV+LNPM+W 
Sbjct: 123 IGGVSGSDLPGSEGGEIVRMFRDYLGHSSFILPPLPNTLFTRDTTCWIYGGVSLNPMHWT 182

Query: 184 ARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGER 243
           ARRQETLLT AIY+FHP+F + +F++WYGDP+ DHG +TLEGGDVMPIG GVVLIGMGER
Sbjct: 183 ARRQETLLTAAIYRFHPQFRDQDFKVWYGDPELDHGLATLEGGDVMPIGKGVVLIGMGER 242

Query: 244 SSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVP 303
           SSRQAIGQ+AQSLF  GAAERVIVAGLP+SR+AMHLDTVFSFCDRDLVT+FPEVV  I  
Sbjct: 243 SSRQAIGQLAQSLFRHGAAERVIVAGLPRSRSAMHLDTVFSFCDRDLVTIFPEVVHGITA 302

Query: 304 FSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVC 363
           FSLRPD   P G+++RRE+  FL+VVAE+LGL  LRVVETGG+S+  EREQWDDGNNVV 
Sbjct: 303 FSLRPDERKPDGIDLRREQAPFLDVVAEALGLTALRVVETGGDSYEVEREQWDDGNNVVA 362

Query: 364 LEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPIDY 418
           LEPGVV+GYDRNT+TNT+LRKAGVEVITISASELGRGRGGGHCMTCPI+RD IDY
Sbjct: 363 LEPGVVIGYDRNTFTNTMLRKAGVEVITISASELGRGRGGGHCMTCPIIRDAIDY 417


Lambda     K      H
   0.319    0.137    0.414 

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: 680
Number of extensions: 20
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: 418
Length of database: 417
Length adjustment: 32
Effective length of query: 386
Effective length of database: 385
Effective search space:   148610
Effective search space used:   148610
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 GFF271 Psest_0272 (arginine deiminase)
to HMM TIGR01078 (arcA: arginine deiminase (EC 3.5.3.6))

# 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/TIGR01078.hmm
# target sequence database:        /tmp/gapView.4477.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01078  [M=408]
Accession:   TIGR01078
Description: arcA: arginine deiminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.7e-168  545.9   0.0     3e-168  545.7   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF271  Psest_0272 arginine deiminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF271  Psest_0272 arginine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.7   0.0    3e-168    3e-168       3     408 .]       9     415 ..       7     415 .. 0.99

  Alignments for each domain:
  == domain 1  score: 545.7 bits;  conditional E-value: 3e-168
                          TIGR01078   3 vysEiGkLkkvllhrPgkelenltPsnldelLFddilavedakkeHdeFveklrdngvevllledLlaEtlaasea 78 
                                        v+sE+GkL+kv++++Pg ++++ltPsn+delLFdd+l+v++ak++H +Fv+k+r++gvevl++++Ll+Etl+ +ea
  lcl|FitnessBrowser__psRCH2:GFF271   9 VHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVLWVSQAKRDHFDFVSKMRERGVEVLEMHNLLTETLSDPEA 84 
                                        9*************************************************************************** PP

                          TIGR01078  79 keklldealeeaeilgeelkkelreylksletrelvekllaGvakeelpeeedselslvdlevegdsefvidPlPn 154
                                         ++lld+++++++ +g +l+ e+r++l+ le r+l+e l++Gv  ++lp +e  e+ ++ + + g+s+f+++PlPn
  lcl|FitnessBrowser__psRCH2:GFF271  85 LKWLLDRKITANQ-VGLGLQGEVRSWLEGLERRQLAEFLIGGVSGSDLPGSEGGEIVRMFRDYLGHSSFILPPLPN 159
                                        *************.9************************************************************* PP

                          TIGR01078 155 llFtRDpsasigngvtlnkmalkaRqrEtlftelifkhHpkfanaevevyyd....rsekaslEGGDvlvlskdvl 226
                                        +lFtRD++++i++gv+ln+m + aR++Etl+t +i+++Hp+f +++++v+y+    ++  a+lEGGDv+ ++k+v+
  lcl|FitnessBrowser__psRCH2:GFF271 160 TLFTRDTTCWIYGGVSLNPMHWTARRQETLLTAAIYRFHPQFRDQDFKVWYGdpelDHGLATLEGGDVMPIGKGVV 235
                                        ***************************************************999999999**************** PP

                          TIGR01078 227 viGiseRtsaqsveklakslfkneaefkkvlaiklpkkralmHLDtvltmvDkdkftvfpevekelkafsiysltk 302
                                        +iG++eR+s+q++++la+slf + +++++v+++ lp++r++mHLDtv++++D+d +t+fpev++ ++afs++ +++
  lcl|FitnessBrowser__psRCH2:GFF271 236 LIGMGERSSRQAIGQLAQSLFRH-GAAERVIVAGLPRSRSAMHLDTVFSFCDRDLVTIFPEVVHGITAFSLRPDER 310
                                        ***********************.**************************************************** PP

                          TIGR01078 303 gneekikveekakleevlaealgvkklkliktgGgdsveaeREqwnDgnnvlaiaPGvvvaYeRnvvtnallekaG 378
                                        ++++   ++e+a++ +v+aealg+  l++++tg gds+e eREqw+Dgnnv+a++PGvv++Y+Rn+ tn++l+kaG
  lcl|FitnessBrowser__psRCH2:GFF271 311 KPDGIDLRREQAPFLDVVAEALGLTALRVVETG-GDSYEVEREQWDDGNNVVALEPGVVIGYDRNTFTNTMLRKAG 385
                                        *********************************.9***************************************** PP

                          TIGR01078 379 ikvltiagseLsrGrGgprCmsmplvRddi 408
                                        ++v+ti++seL+rGrGg++Cm++p+ Rd i
  lcl|FitnessBrowser__psRCH2:GFF271 386 VEVITISASELGRGRGGGHCMTCPIIRDAI 415
                                        ***************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (408 nodes)
Target sequences:                          1  (417 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: 10.25
//
[ok]

This GapMind analysis is from Sep 17 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