Alignments for a candidate for arcA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcA in Pseudomonas fluorescens GW456-L13

Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate PfGW456L13_1874 Arginine deiminase (EC 3.5.3.6)

Query= BRENDA::P13981
         (418 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874
          Length = 418

 Score =  718 bits (1853), Expect = 0.0
 Identities = 343/418 (82%), Positives = 380/418 (90%)

Query: 1   MSTEKTKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVT 60
           M+TEK K GVHSEAGKLRKVMVCSPGLAHQRLTP+NCDELLFDDV+WV QAKRDHFDFVT
Sbjct: 1   MTTEKVKYGVHSEAGKLRKVMVCSPGLAHQRLTPNNCDELLFDDVLWVAQAKRDHFDFVT 60

Query: 61  KMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLA 120
           KMRER IDVLEMHNLLT+ +  PEAL WIL+RK+TA+SVGLGL +E  SWL SLEPRK+A
Sbjct: 61  KMRERNIDVLEMHNLLTDIVAIPEALDWILERKVTANSVGLGLINETSSWLRSLEPRKIA 120

Query: 121 EYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPM 180
           E+LIGGV+ DDLP+S G   ++M+R++LG+SSF+LPPLPNTQFTRDTTCWIYGGVTLNPM
Sbjct: 121 EFLIGGVSGDDLPSSFGGKAIEMFRDFLGNSSFILPPLPNTQFTRDTTCWIYGGVTLNPM 180

Query: 181 YWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGM 240
           YWPARRQETLLTTAIYKFHPEF  A+FEIWYGDPD DHG+STLEGGDVMPIGNGVVLIGM
Sbjct: 181 YWPARRQETLLTTAIYKFHPEFTKADFEIWYGDPDLDHGNSTLEGGDVMPIGNGVVLIGM 240

Query: 241 GERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKE 300
           GERSSRQAI Q+A +LF   A E+VIVAGLPKSRAAMHLDTVFSFCDRDLVT+FPEVV +
Sbjct: 241 GERSSRQAIAQLAVNLFKNKAVEKVIVAGLPKSRAAMHLDTVFSFCDRDLVTIFPEVVNQ 300

Query: 301 IVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNN 360
           IV F+LRPD S   G++IRREE +FL+ VA++L LK LRVVETGGNSFAAEREQWDDGNN
Sbjct: 301 IVAFTLRPDESKAGGIDIRREETSFLDTVAQALNLKALRVVETGGNSFAAEREQWDDGNN 360

Query: 361 VVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPIDY 418
           VV +EPGVV+GYDRNTYTNTLLRKAGVEVITISA ELGRGRGGGHCMTCPI+RDPIDY
Sbjct: 361 VVAVEPGVVIGYDRNTYTNTLLRKAGVEVITISAGELGRGRGGGHCMTCPIIRDPIDY 418


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: 672
Number of extensions: 14
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: 418
Length adjustment: 32
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
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 PfGW456L13_1874 (Arginine deiminase (EC 3.5.3.6))
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.18897.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
     1e-166  540.6   0.0   1.2e-166  540.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874  Arginine deiminase (EC 3.5.3.6)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874  Arginine deiminase (EC 3.5.3.6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.4   0.0  1.2e-166  1.2e-166       3     408 .]      10     416 ..       8     416 .. 0.99

  Alignments for each domain:
  == domain 1  score: 540.4 bits;  conditional E-value: 1.2e-166
                                               TIGR01078   3 vysEiGkLkkvllhrPgkelenltPsnldelLFddilavedakkeHdeFveklrd 57 
                                                             v+sE+GkL+kv++++Pg ++++ltP+n+delLFdd+l+v +ak++H +Fv+k+r+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874  10 VHSEAGKLRKVMVCSPGLAHQRLTPNNCDELLFDDVLWVAQAKRDHFDFVTKMRE 64 
                                                             99***************************************************** PP

                                               TIGR01078  58 ngvevllledLlaEtlaaseakeklldealeeaeilgeelkkelreylksletre 112
                                                             ++++vl++++Ll++ +a++ea +++l++++++++ +g +l +e +++l+sle+r+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874  65 RNIDVLEMHNLLTDIVAIPEALDWILERKVTANS-VGLGLINETSSWLRSLEPRK 118
                                                             **********************************.9******************* PP

                                               TIGR01078 113 lvekllaGvakeelpeeedselslvdlevegdsefvidPlPnllFtRDpsasign 167
                                                             ++e l++Gv  ++lp++   +   + +   g+s+f+++PlPn++FtRD++++i++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874 119 IAEFLIGGVSGDDLPSSFGGKAIEMFRDFLGNSSFILPPLPNTQFTRDTTCWIYG 173
                                                             ******************************************************* PP

                                               TIGR01078 168 gvtlnkmalkaRqrEtlftelifkhHpkfanaevevyyd....rsekaslEGGDv 218
                                                             gvtln+m+++aR++Etl+t++i+k+Hp+f++a++e++y+    ++ +++lEGGDv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874 174 GVTLNPMYWPARRQETLLTTAIYKFHPEFTKADFEIWYGdpdlDHGNSTLEGGDV 228
                                                             **************************************9999999********** PP

                                               TIGR01078 219 lvlskdvlviGiseRtsaqsveklakslfkneaefkkvlaiklpkkralmHLDtv 273
                                                             + ++++v++iG++eR+s+q++ +la +lfkn ++++kv+++ lpk+ra+mHLDtv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874 229 MPIGNGVVLIGMGERSSRQAIAQLAVNLFKN-KAVEKVIVAGLPKSRAAMHLDTV 282
                                                             *******************************.99********************* PP

                                               TIGR01078 274 ltmvDkdkftvfpevekelkafsiysltkgneekikveekakleevlaealgvkk 328
                                                             ++++D+d +t+fpev+++++af+++ ++++  +  +++e++++ + +a+al++k 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874 283 FSFCDRDLVTIFPEVVNQIVAFTLRPDESKAGGIDIRREETSFLDTVAQALNLKA 337
                                                             ******************************99999******************** PP

                                               TIGR01078 329 lkliktgGgdsveaeREqwnDgnnvlaiaPGvvvaYeRnvvtnallekaGikvlt 383
                                                             l++++tg g+s++aeREqw+Dgnnv+a++PGvv++Y+Rn++tn+ll+kaG++v+t
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874 338 LRVVETG-GNSFAAEREQWDDGNNVVAVEPGVVIGYDRNTYTNTLLRKAGVEVIT 391
                                                             ******9.9********************************************** PP

                                               TIGR01078 384 iagseLsrGrGgprCmsmplvRddi 408
                                                             i++ eL+rGrGg++Cm++p+ Rd+i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874 392 ISAGELGRGRGGGHCMTCPIIRDPI 416
                                                             **********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (408 nodes)
Target sequences:                          1  (418 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: 9.35
//
[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