Alignments for a candidate for adiA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Shewanella oneidensis MR-1

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 201032 SO1870 biosynthetic arginine decarboxylase (NCBI ptt file)

Query= BRENDA::Q7MK24
         (640 letters)



>FitnessBrowser__MR1:201032
          Length = 637

 Score =  887 bits (2291), Expect = 0.0
 Identities = 433/631 (68%), Positives = 523/631 (82%), Gaps = 1/631 (0%)

Query: 11  LDRVRADYNVHYWSQGFYGIDDQGEMYVSPRSDNA-HQIQLSKIVKQLEERQLNVPVLVR 69
           ++  RA YNV +WSQGFYGI D+GE+ VSP   N  H+I L+++ K + +  + +PVLVR
Sbjct: 6   IEAARAGYNVTHWSQGFYGISDEGEVTVSPDPKNPDHKIGLNELAKDMVKAGVALPVLVR 65

Query: 70  FPQILHQRVHSICDAFNQAIEEYQYPNKYLLVYPIKVNQQREVVDEILASQAQLETKQLG 129
           FPQILH RV+S+C AF+QAI++Y+Y   YLLVYPIKVNQQ+ VV+EILASQA  E  QLG
Sbjct: 66  FPQILHHRVNSLCQAFDQAIQKYEYQADYLLVYPIKVNQQKTVVEEILASQASKEVPQLG 125

Query: 130 LEAGSKPELLAVLAMAQHASSVIVCNGYKDREYIRLALIGEKLGHKVFIVLEKMSELDLV 189
           LEAGSKPEL+AVLAMAQ ASSVIVCNGYKD EYIRLALIGEKLGHKV+IVLEK+SEL +V
Sbjct: 126 LEAGSKPELMAVLAMAQKASSVIVCNGYKDNEYIRLALIGEKLGHKVYIVLEKLSELKMV 185

Query: 190 LREAKSLGVTPRLGIRIRLASQGAGKWQASGGEKSKFGLSASQVLNVISRLKKENQLDTL 249
           L E+K LGV PRLG+R RLA QG GKWQASGGEKSKFGLSA+Q+L V+ +LK+ + LD+L
Sbjct: 186 LAESKRLGVKPRLGLRARLAFQGKGKWQASGGEKSKFGLSAAQILTVVDQLKQSDMLDSL 245

Query: 250 QLVHFHLGSQMANIRDVRNGVNESARFYCELRTLGANITYFDVGGGLAIDYDGTRSQSSN 309
           QL+HFHLGSQ+ANIRD+R GV+E+ARFYCELR LGA+I  FDVGGGLA+DYDGTRSQS+N
Sbjct: 246 QLLHFHLGSQIANIRDIRQGVSEAARFYCELRELGASINCFDVGGGLAVDYDGTRSQSNN 305

Query: 310 SMNYGLVEYARNIVNTVGDVCKDYKQPMPVIISESGRSLTAHHAVLISNVIGTETYKPET 369
           SMNYGL EYA NIVN + D+C +Y+QPMP IISESGR LTAHHAVLI++VIGTE Y+ E 
Sbjct: 306 SMNYGLSEYANNIVNVLTDICNEYEQPMPRIISESGRHLTAHHAVLITDVIGTEAYQVED 365

Query: 370 VTEPEEDFPLLLNNMWRSWLNLHNGTDARALIEIYNDTQSDLAEVHSQFATGVLTLEHRA 429
           +  PEE+ P LL+NMW+SW  L    D RALIEIY+D+QSDL E  S FA G L+L  RA
Sbjct: 366 IQPPEEESPQLLHNMWQSWTELSGRADQRALIEIYHDSQSDLQEAQSLFALGQLSLAERA 425

Query: 430 WAEQTSLRIYYELNRLMSTKNRFHRPILDELSERLADKFFVNFSLFQSLPDSWGIDQVFP 489
           WAEQ +LR+ +E+  L+STKNR+HRPI+DEL+E+LADKFFVNFSLFQSLPD+WGIDQVFP
Sbjct: 426 WAEQANLRVCHEVQGLLSTKNRYHRPIIDELNEKLADKFFVNFSLFQSLPDAWGIDQVFP 485

Query: 490 VLPLSGLQNAADRRAVMLDITCDSDGAIDAYVDGQGIESTLPVPAWNEDEPYLMGFFLVG 549
           VLPLSGL  A +RRAVMLDITCDSDG +D YVDGQGIE+TLPVPAW+ + PYL+GFF+VG
Sbjct: 486 VLPLSGLDKAPERRAVMLDITCDSDGIVDQYVDGQGIETTLPVPAWSAESPYLIGFFMVG 545

Query: 550 AYQEILGDMHNLFGDTHSVVVNVGDQGEINIDFINEGDTVEDMMRYVHIDVDQIRKNYHS 609
           AYQEILGDMHNLFGDT+S VV++ + G  NI+ +  GDTV D++RYV++D     + Y  
Sbjct: 546 AYQEILGDMHNLFGDTNSAVVSIEENGMTNIESVLAGDTVADVLRYVNLDAVDFMRTYEE 605

Query: 610 LVSQRVDQEEQQQILAELEQGLSGYTYLEDF 640
           LV+Q + ++E+ QIL EL+ GL GYTYLEDF
Sbjct: 606 LVNQHIAEDERAQILEELQVGLKGYTYLEDF 636


Lambda     K      H
   0.318    0.135    0.392 

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: 1154
Number of extensions: 45
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: 640
Length of database: 637
Length adjustment: 38
Effective length of query: 602
Effective length of database: 599
Effective search space:   360598
Effective search space used:   360598
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 201032 SO1870 (biosynthetic arginine decarboxylase (NCBI ptt file))
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.13628.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.2e-269  880.6   0.1   3.6e-269  880.4   0.1    1.0  1  lcl|FitnessBrowser__MR1:201032  SO1870 biosynthetic arginine dec


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201032  SO1870 biosynthetic arginine decarboxylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  880.4   0.1  3.6e-269  3.6e-269       1     624 []       4     634 ..       4     634 .. 0.98

  Alignments for each domain:
  == domain 1  score: 880.4 bits;  conditional E-value: 3.6e-269
                       TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslnaaFk 79 
                                     ws+e +++ Yn+++W++g++ + +eGev+v+p+ ++  ++i l el k++ ++g+ lP+lvrFp+il++r++sl++aF+
  lcl|FitnessBrowser__MR1:201032   4 WSIEAARAGYNVTHWSQGFYGISDEGEVTVSPDPKNPDHKIGLNELAKDMVKAGVALPVLVRFPQILHHRVNSLCQAFD 82 
                                     78999999*********************************************************************** PP

                       TIGR01273  80 eaieeleYaskyqavyPiKvnqqrevveelvasg....gkslGLEaGsKpEllialalaekpkavivcnGyKDreyiel 154
                                     +ai+++eY+++y +vyPiKvnqq++vvee++as+      +lGLEaGsKpEl+++la+a+k+++vivcnGyKD+eyi+l
  lcl|FitnessBrowser__MR1:201032  83 QAIQKYEYQADYLLVYPIKVNQQKTVVEEILASQaskeVPQLGLEAGSKPELMAVLAMAQKASSVIVCNGYKDNEYIRL 161
                                     ********************************9986434589************************************* PP

                       TIGR01273 155 aliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvkklkeed 233
                                     ali++klg+kv+iv+ekl+El++v++e+k+lgvkP+lGlR+rLa +g gkw+ sgGeksKFGLsa+q+l+vv++lk++d
  lcl|FitnessBrowser__MR1:201032 162 ALIGEKLGHKVYIVLEKLSELKMVLAESKRLGVKPRLGLRARLAFQGKGKWQASGGEKSKFGLSAAQILTVVDQLKQSD 240
                                     ******************************************************************************* PP

                       TIGR01273 234 lldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavv 312
                                     +ldsl+llHfHlGsqiani+d+++gv+Eaar+y+elr+lG++i+++dvGGGL+vdYdGt+s+s++s+nY+l eya+++v
  lcl|FitnessBrowser__MR1:201032 241 MLDSLQLLHFHLGSQIANIRDIRQGVSEAARFYCELRELGASINCFDVGGGLAVDYDGTRSQSNNSMNYGLSEYANNIV 319
                                     ******************************************************************************* PP

                       TIGR01273 313 aalkevceekgvpePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevk....eleellkeideesae 387
                                      +l ++c+e+++p P+iisEsGR +tahhavl+++v+++e+++ e+  ++ eee+p++++    +++el++ +d+++++
  lcl|FitnessBrowser__MR1:201032 320 NVLTDICNEYEQPMPRIISESGRHLTAHHAVLITDVIGTEAYQVED-IQPPEEESPQLLHnmwqSWTELSGRADQRALI 397
                                     *****************************************99995.45566799999998888899************ PP

                       TIGR01273 388 elledavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaekylvnlslFqslPD 465
                                     e+++d++++l+ea +lf+lG+l+l+era+aeq  l+++++v+  l++k++ hr+i+del+ekla+k++vn+slFqslPD
  lcl|FitnessBrowser__MR1:201032 398 EIYHDSQSDLQEAQSLFALGQLSLAERAWAEQANLRVCHEVQGlLSTKNRYHRPIIDELNEKLADKFFVNFSLFQSLPD 476
                                     *******************************************99********************************** PP

                       TIGR01273 466 aWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvH 544
                                     aWgidq+fP+lPl++Ld++p+rrav+lD+tCDsDG ++++v++qgie+tlp+++++ + +yl+gff+vGAYqEiLgd+H
  lcl|FitnessBrowser__MR1:201032 477 AWGIDQVFPVLPLSGLDKAPERRAVMLDITCDSDGIVDQYVDGQGIETTLPVPAWSAESPYLIGFFMVGAYQEILGDMH 555
                                     ******************************************************************************* PP

                       TIGR01273 545 nLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkaeekkqvlelleaglsgypYL 623
                                     nLFgdt+++ v ++e+g +++e++  gdtv+dvl++v++d+ + ++++++ v++ +++++e++q+le+l++gl+gy+YL
  lcl|FitnessBrowser__MR1:201032 556 NLFGDTNSAVVSIEENGMTNIESVLAGDTVADVLRYVNLDAVDFMRTYEELVNQ-HIAEDERAQILEELQVGLKGYTYL 633
                                     ***************************************************998.599********************9 PP

                       TIGR01273 624 s 624
                                     +
  lcl|FitnessBrowser__MR1:201032 634 E 634
                                     6 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.54
//
[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