Alignments for a candidate for adiA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Pseudomonas stutzeri RCH2

Align Biosynthetic arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate GFF3302 Psest_3366 arginine decarboxylase, biosynthetic

Query= reanno::psRCH2:GFF3302
         (637 letters)



>FitnessBrowser__psRCH2:GFF3302
          Length = 637

 Score = 1266 bits (3277), Expect = 0.0
 Identities = 637/637 (100%), Positives = 637/637 (100%)

Query: 1   MPVRRTRKDDGSQWTAADSRSIYGIRHWGAGYFAISDEGNVEVRPQGPSGEPIEFNGLIE 60
           MPVRRTRKDDGSQWTAADSRSIYGIRHWGAGYFAISDEGNVEVRPQGPSGEPIEFNGLIE
Sbjct: 1   MPVRRTRKDDGSQWTAADSRSIYGIRHWGAGYFAISDEGNVEVRPQGPSGEPIEFNGLIE 60

Query: 61  QLREAGLSLPLLVRFPGILQDRVRRLTGAFDANIERMEYAGKYTALYPIKVNQQEAVVEN 120
           QLREAGLSLPLLVRFPGILQDRVRRLTGAFDANIERMEYAGKYTALYPIKVNQQEAVVEN
Sbjct: 61  QLREAGLSLPLLVRFPGILQDRVRRLTGAFDANIERMEYAGKYTALYPIKVNQQEAVVEN 120

Query: 121 IIATQNVSIGLEAGSKPELMAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHKVFIVI 180
           IIATQNVSIGLEAGSKPELMAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHKVFIVI
Sbjct: 121 IIATQNVSIGLEAGSKPELMAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHKVFIVI 180

Query: 181 EKESEVGLVIEEANELKLTPQVGLRVRLSSLASSKWADTGGERSKFGLSAAQLLSVIERF 240
           EKESEVGLVIEEANELKLTPQVGLRVRLSSLASSKWADTGGERSKFGLSAAQLLSVIERF
Sbjct: 181 EKESEVGLVIEEANELKLTPQVGLRVRLSSLASSKWADTGGERSKFGLSAAQLLSVIERF 240

Query: 241 RAAEMDQGIRLLHFHMGSQIANLADYRQGFREAIRYYAELRALNLPVDYIDVGGGLGVDY 300
           RAAEMDQGIRLLHFHMGSQIANLADYRQGFREAIRYYAELRALNLPVDYIDVGGGLGVDY
Sbjct: 241 RAAEMDQGIRLLHFHMGSQIANLADYRQGFREAIRYYAELRALNLPVDYIDVGGGLGVDY 300

Query: 301 DGTHSRNASSINYDIDEYAGTVVGMLKEFCEAQGLPHPNIFSESGRAMTAHHAVLVMQVT 360
           DGTHSRNASSINYDIDEYAGTVVGMLKEFCEAQGLPHPNIFSESGRAMTAHHAVLVMQVT
Sbjct: 301 DGTHSRNASSINYDIDEYAGTVVGMLKEFCEAQGLPHPNIFSESGRAMTAHHAVLVMQVT 360

Query: 361 DVERHNDELPVIENYDELPEIVQSLADLLGPTDPEMVTETYWRATHYMSESSAQYASGKL 420
           DVERHNDELPVIENYDELPEIVQSLADLLGPTDPEMVTETYWRATHYMSESSAQYASGKL
Sbjct: 361 DVERHNDELPVIENYDELPEIVQSLADLLGPTDPEMVTETYWRATHYMSESSAQYASGKL 420

Query: 421 TLAQKALAEQSYFAICRRLYNQLKARQRSHRAVLDELNDKLADKYICNFSVFQSLPDTWA 480
           TLAQKALAEQSYFAICRRLYNQLKARQRSHRAVLDELNDKLADKYICNFSVFQSLPDTWA
Sbjct: 421 TLAQKALAEQSYFAICRRLYNQLKARQRSHRAVLDELNDKLADKYICNFSVFQSLPDTWA 480

Query: 481 IDQILPIVPLQRLSEEPVRRAVLQDLTCDSDGKIKHYVDEQSIESSMPVHEVAPGEEYFL 540
           IDQILPIVPLQRLSEEPVRRAVLQDLTCDSDGKIKHYVDEQSIESSMPVHEVAPGEEYFL
Sbjct: 481 IDQILPIVPLQRLSEEPVRRAVLQDLTCDSDGKIKHYVDEQSIESSMPVHEVAPGEEYFL 540

Query: 541 GVFLVGAYQEILGDMHNLFGDTDSVNVYQREDGSYYHAGIETHDTIEDMLRYVHLSPEEL 600
           GVFLVGAYQEILGDMHNLFGDTDSVNVYQREDGSYYHAGIETHDTIEDMLRYVHLSPEEL
Sbjct: 541 GVFLVGAYQEILGDMHNLFGDTDSVNVYQREDGSYYHAGIETHDTIEDMLRYVHLSPEEL 600

Query: 601 MTYYRDKVASAKLSAKERTQYIDALRLGLTRSSYLTP 637
           MTYYRDKVASAKLSAKERTQYIDALRLGLTRSSYLTP
Sbjct: 601 MTYYRDKVASAKLSAKERTQYIDALRLGLTRSSYLTP 637


Lambda     K      H
   0.318    0.135    0.391 

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: 1418
Number of extensions: 39
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: 637
Length of database: 637
Length adjustment: 38
Effective length of query: 599
Effective length of database: 599
Effective search space:   358801
Effective search space used:   358801
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate GFF3302 Psest_3366 (arginine decarboxylase, biosynthetic)
to HMM TIGR01273 (speA: arginine decarboxylase (EC 4.1.1.19))

# 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/TIGR01273.hmm
# target sequence database:        /tmp/gapView.22707.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01273  [M=624]
Accession:   TIGR01273
Description: speA: arginine decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.8e-269  880.8   0.0   3.1e-269  880.6   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3302  Psest_3366 arginine decarboxylas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3302  Psest_3366 arginine decarboxylase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  880.6   0.0  3.1e-269  3.1e-269       1     624 []      14     636 ..      14     636 .. 0.99

  Alignments for each domain:
  == domain 1  score: 880.6 bits;  conditional E-value: 3.1e-269
                           TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkriksln 75 
                                         w+a++s+++Y+i++Wgagyfa+ +eG+v+vrp+g +  + i+   l++q++++gl+lPllvrFp ilq+r+++l+
  lcl|FitnessBrowser__psRCH2:GFF3302  14 WTAADSRSIYGIRHWGAGYFAISDEGNVEVRPQGPS-GEPIEFNGLIEQLREAGLSLPLLVRFPGILQDRVRRLT 87 
                                         88999***************************9888.9************************************* PP

                           TIGR01273  76 aaFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpEllialalaekpkavivcnGyKDre 150
                                          aF+++ie++eYa+ky+a+yPiKvnqq++vve+++a+++ s+GLEaGsKpEl+++lala  ++ +ivcnGyKDre
  lcl|FitnessBrowser__psRCH2:GFF3302  88 GAFDANIERMEYAGKYTALYPIKVNQQEAVVENIIATQNVSIGLEAGSKPELMAVLALAP-KGGTIVCNGYKDRE 161
                                         ************************************************************.8899********** PP

                           TIGR01273 151 yielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlev 225
                                         +i+lal+++klg+kv+iviek++E+ lvieea++l+ +P++GlRvrL+s +s+kwa++gGe+sKFGLsa+q+l+v
  lcl|FitnessBrowser__psRCH2:GFF3302 162 FIRLALMGQKLGHKVFIVIEKESEVGLVIEEANELKLTPQVGLRVRLSSLASSKWADTGGERSKFGLSAAQLLSV 236
                                         *************************************************************************** PP

                           TIGR01273 226 vkklkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsv 300
                                         +++++++++++ ++llHfH+Gsqian++d+++g+rEa+r+y+elr l ++++++dvGGGLgvdYdGt+s++++s+
  lcl|FitnessBrowser__psRCH2:GFF3302 237 IERFRAAEMDQGIRLLHFHMGSQIANLADYRQGFREAIRYYAELRALNLPVDYIDVGGGLGVDYDGTHSRNASSI 311
                                         *************************************************************************** PP

                           TIGR01273 301 nYsleeyaaavvaalkevceekgvpePviisEsGRaitahhavlvaevleveeeeeee.aeeile.eeapeevke 373
                                         nY+++eya +vv +lke+ce++g+p+P+i+sEsGRa+tahhavlv++v++ve++++e  + e  + +e pe+v++
  lcl|FitnessBrowser__psRCH2:GFF3302 312 NYDIDEYAGTVVGMLKEFCEAQGLPHPNIFSESGRAMTAHHAVLVMQVTDVERHNDELpVIE--NyDELPEIVQS 384
                                         *******************************************************9954444..3469******* PP

                           TIGR01273 374 leellkeideesaeelledavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqe 447
                                         l++ll+++d e+++e++++a+++++e  +++++Gkl+l+++alaeq + ai++++ + l+a+++shr +ldel++
  lcl|FitnessBrowser__psRCH2:GFF3302 385 LADLLGPTDPEMVTETYWRATHYMSESSAQYASGKLTLAQKALAEQSYFAICRRLYNqLKARQRSHRAVLDELND 459
                                         ******************************************************9988***************** PP

                           TIGR01273 448 klaekylvnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldk 522
                                         kla+ky++n+s+FqslPD+W+idq++Pi+Pl+rL e+p rravl+DltCDsDGkik++v+eq+ie+++p+he+ +
  lcl|FitnessBrowser__psRCH2:GFF3302 460 KLADKYICNFSVFQSLPDTWAIDQILPIVPLQRLSEEPVRRAVLQDLTCDSDGKIKHYVDEQSIESSMPVHEVAP 534
                                         *************************************************************************** PP

                           TIGR01273 523 deeyllgfflvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkva 597
                                          eey+lg+flvGAYqEiLgd+HnLFgdt++v+v+++e+g+++++ ie++dt+ed+l++v+++peel++ +++kva
  lcl|FitnessBrowser__psRCH2:GFF3302 535 GEEYFLGVFLVGAYQEILGDMHNLFGDTDSVNVYQREDGSYYHAGIETHDTIEDMLRYVHLSPEELMTYYRDKVA 609
                                         *************************************************************************** PP

                           TIGR01273 598 eaklkaeekkqvlelleaglsgypYLs 624
                                         +akl+a+e++q++++l+ gl++++YL+
  lcl|FitnessBrowser__psRCH2:GFF3302 610 SAKLSAKERTQYIDALRLGLTRSSYLT 636
                                         *************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (637 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.88
//
[ok]

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

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