Alignments for a candidate for adiA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Escherichia coli BW25113

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 17017 b2938 arginine decarboxylase (NCBI)

Query= BRENDA::P21170
         (658 letters)



>FitnessBrowser__Keio:17017
          Length = 658

 Score = 1331 bits (3445), Expect = 0.0
 Identities = 658/658 (100%), Positives = 658/658 (100%)

Query: 1   MSDDMSMGLPSSAGEHGVLRSMQEVAMSSQEASKMLRTYNIAWWGNNYYDVNELGHISVC 60
           MSDDMSMGLPSSAGEHGVLRSMQEVAMSSQEASKMLRTYNIAWWGNNYYDVNELGHISVC
Sbjct: 1   MSDDMSMGLPSSAGEHGVLRSMQEVAMSSQEASKMLRTYNIAWWGNNYYDVNELGHISVC 60

Query: 61  PDPDVPEARVDLAQLVKTREAQGQRLPALFCFPQILQHRLRSINAAFKRARESYGYNGDY 120
           PDPDVPEARVDLAQLVKTREAQGQRLPALFCFPQILQHRLRSINAAFKRARESYGYNGDY
Sbjct: 61  PDPDVPEARVDLAQLVKTREAQGQRLPALFCFPQILQHRLRSINAAFKRARESYGYNGDY 120

Query: 121 FLVYPIKVNQHRRVIESLIHSGEPLGLEAGSKAELMAVLAHAGMTRSVIVCNGYKDREYI 180
           FLVYPIKVNQHRRVIESLIHSGEPLGLEAGSKAELMAVLAHAGMTRSVIVCNGYKDREYI
Sbjct: 121 FLVYPIKVNQHRRVIESLIHSGEPLGLEAGSKAELMAVLAHAGMTRSVIVCNGYKDREYI 180

Query: 181 RLALIGEKMGHKVYLVIEKMSEIAIVLDEAERLNVVPRLGVRARLASQGSGKWQSSGGEK 240
           RLALIGEKMGHKVYLVIEKMSEIAIVLDEAERLNVVPRLGVRARLASQGSGKWQSSGGEK
Sbjct: 181 RLALIGEKMGHKVYLVIEKMSEIAIVLDEAERLNVVPRLGVRARLASQGSGKWQSSGGEK 240

Query: 241 SKFGLAATQVLQLVETLREAGRLDSLQLLHFHLGSQMANIRDIATGVRESARFYVELHKL 300
           SKFGLAATQVLQLVETLREAGRLDSLQLLHFHLGSQMANIRDIATGVRESARFYVELHKL
Sbjct: 241 SKFGLAATQVLQLVETLREAGRLDSLQLLHFHLGSQMANIRDIATGVRESARFYVELHKL 300

Query: 301 GVNIQCFDVGGGLGVDYEGTRSQSDCSVNYGLNEYANNIIWAIGDACEENGLPHPTVITE 360
           GVNIQCFDVGGGLGVDYEGTRSQSDCSVNYGLNEYANNIIWAIGDACEENGLPHPTVITE
Sbjct: 301 GVNIQCFDVGGGLGVDYEGTRSQSDCSVNYGLNEYANNIIWAIGDACEENGLPHPTVITE 360

Query: 361 SGRAVTAHHTVLVSNIIGVERNEYTVPTAPAEDAPRALQSMWETWQEMHEPGTRRSLREW 420
           SGRAVTAHHTVLVSNIIGVERNEYTVPTAPAEDAPRALQSMWETWQEMHEPGTRRSLREW
Sbjct: 361 SGRAVTAHHTVLVSNIIGVERNEYTVPTAPAEDAPRALQSMWETWQEMHEPGTRRSLREW 420

Query: 421 LHDSQMDLHDIHIGYSSGIFSLQERAWAEQLYLSMCHEVQKQLDPQNRAHRPIIDELQER 480
           LHDSQMDLHDIHIGYSSGIFSLQERAWAEQLYLSMCHEVQKQLDPQNRAHRPIIDELQER
Sbjct: 421 LHDSQMDLHDIHIGYSSGIFSLQERAWAEQLYLSMCHEVQKQLDPQNRAHRPIIDELQER 480

Query: 481 MADKMYVNFSLFQSMPDAWGIDQLFPVLPLEGLDQVPERRAVLLDITCDSDGAIDHYIDG 540
           MADKMYVNFSLFQSMPDAWGIDQLFPVLPLEGLDQVPERRAVLLDITCDSDGAIDHYIDG
Sbjct: 481 MADKMYVNFSLFQSMPDAWGIDQLFPVLPLEGLDQVPERRAVLLDITCDSDGAIDHYIDG 540

Query: 541 DGIATTMPMPEYDPENPPMLGFFMVGAYQEILGNMHNLFGDTEAVDVFVFPDGSVEVELS 600
           DGIATTMPMPEYDPENPPMLGFFMVGAYQEILGNMHNLFGDTEAVDVFVFPDGSVEVELS
Sbjct: 541 DGIATTMPMPEYDPENPPMLGFFMVGAYQEILGNMHNLFGDTEAVDVFVFPDGSVEVELS 600

Query: 601 DEGDTVADMLQYVQLDPKTLLTQFRDQVKKTDLDAELQQQFLEEFEAGLYGYTYLEDE 658
           DEGDTVADMLQYVQLDPKTLLTQFRDQVKKTDLDAELQQQFLEEFEAGLYGYTYLEDE
Sbjct: 601 DEGDTVADMLQYVQLDPKTLLTQFRDQVKKTDLDAELQQQFLEEFEAGLYGYTYLEDE 658


Lambda     K      H
   0.319    0.136    0.404 

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: 1476
Number of extensions: 46
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: 658
Length of database: 658
Length adjustment: 38
Effective length of query: 620
Effective length of database: 620
Effective search space:   384400
Effective search space used:   384400
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: 54 (25.4 bits)

Align candidate 17017 b2938 (arginine decarboxylase (NCBI))
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.31320.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.1e-284  930.1   0.0   3.7e-284  929.9   0.0    1.0  1  lcl|FitnessBrowser__Keio:17017  b2938 arginine decarboxylase (NC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17017  b2938 arginine decarboxylase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  929.9   0.0  3.7e-284  3.7e-284       2     624 .]      31     656 ..      30     656 .. 0.99

  Alignments for each domain:
  == domain 1  score: 929.9 bits;  conditional E-value: 3.7e-284
                       TIGR01273   2 saeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslnaaFke 80 
                                     +a+++ ++Yni++Wg++y++vn+ G++sv+p+ +  ++++dl++lvk+ ea+g++lP l++Fp+ilq+r++s+naaFk+
  lcl|FitnessBrowser__Keio:17017  31 EASKMLRTYNIAWWGNNYYDVNELGHISVCPDPDVPEARVDLAQLVKTREAQGQRLPALFCFPQILQHRLRSINAAFKR 109
                                     578899************************************************************************* PP

                       TIGR01273  81 aieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpEllialalaekpkavivcnGyKDreyielaliar 159
                                     a+e+++Y+++y +vyPiKvnq+r+v+e+l++sg ++lGLEaGsK+El+++la+a ++++vivcnGyKDreyi+lali++
  lcl|FitnessBrowser__Keio:17017 110 ARESYGYNGDYFLVYPIKVNQHRRVIESLIHSG-EPLGLEAGSKAELMAVLAHAGMTRSVIVCNGYKDREYIRLALIGE 187
                                     ********************************6.9******************************************** PP

                       TIGR01273 160 klglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvkklkeedlldsl 238
                                     k+g+kv++viek++E+++v++ea++l+v P+lG+R+rLas+gsgkw+ssgGeksKFGL+a+qvl++v++l+e+++ldsl
  lcl|FitnessBrowser__Keio:17017 188 KMGHKVYLVIEKMSEIAIVLDEAERLNVVPRLGVRARLASQGSGKWQSSGGEKSKFGLAATQVLQLVETLREAGRLDSL 266
                                     ******************************************************************************* PP

                       TIGR01273 239 kllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalke 317
                                     +llHfHlGsq+ani+d+++gvrE+ar+yvel+klGv+i+++dvGGGLgvdY+Gt+s+sd+svnY+l+eya+++++a+ +
  lcl|FitnessBrowser__Keio:17017 267 QLLHFHLGSQMANIRDIATGVRESARFYVELHKLGVNIQCFDVGGGLGVDYEGTRSQSDCSVNYGLNEYANNIIWAIGD 345
                                     ******************************************************************************* PP

                       TIGR01273 318 vceekgvpePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevk....eleellkeideesaeelled 392
                                     +cee+g+p+P++i+EsGRa+tahh+vlv+++++ve++e++  ++++e +ap++++    +++e++++ +++s++e+l+d
  lcl|FitnessBrowser__Keio:17017 346 ACEENGLPHPTVITESGRAVTAHHTVLVSNIIGVERNEYTVPTAPAE-DAPRALQsmweTWQEMHEPGTRRSLREWLHD 423
                                     ****************************************6666655.9*****9999899****************** PP

                       TIGR01273 393 avqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaekylvnlslFqslPDaWgid 470
                                     ++++l++++ ++++G+++l+era+aeql+l+++++v++ l+ ++++hr+i+delqe++a+k++vn+slFqs+PDaWgid
  lcl|FitnessBrowser__Keio:17017 424 SQMDLHDIHIGYSSGIFSLQERAWAEQLYLSMCHEVQKqLDPQNRAHRPIIDELQERMADKMYVNFSLFQSMPDAWGID 502
                                     *************************************99**************************************** PP

                       TIGR01273 471 qlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvHnLFgd 549
                                     qlfP+lPle+Ld+ p+rravllD+tCDsDG+i+++++++gi++t+p++e+d++++ +lgff+vGAYqEiLg++HnLFgd
  lcl|FitnessBrowser__Keio:17017 503 QLFPVLPLEGLDQVPERRAVLLDITCDSDGAIDHYIDGDGIATTMPMPEYDPENPPMLGFFMVGAYQEILGNMHNLFGD 581
                                     ******************************************************************************* PP

                       TIGR01273 550 teavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkaeekkqvlelleaglsgypYLs 624
                                     teav+v+v  +g+veve ++egdtv+d+l++vq+dp++ll++++++v++++l+ae ++q+le++eagl+gy+YL+
  lcl|FitnessBrowser__Keio:17017 582 TEAVDVFVFPDGSVEVELSDEGDTVADMLQYVQLDPKTLLTQFRDQVKKTDLDAELQQQFLEEFEAGLYGYTYLE 656
                                     *************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (658 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.89
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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