Alignments for a candidate for adiA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Stenotrophomonas chelatiphaga DSM 21508

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_057508489.1 ABB28_RS10025 arginine decarboxylase

Query= BRENDA::A0A0H2ZHZ8
         (636 letters)



>NCBI__GCF_001431535.1:WP_057508489.1
          Length = 629

 Score =  588 bits (1516), Expect = e-172
 Identities = 307/626 (49%), Positives = 407/626 (65%), Gaps = 4/626 (0%)

Query: 12  SNWTVADSRGVYGIRHWGAGYFAINDGGNVEVRPQGADSTPIDLYELVGQLREAGLSLPL 71
           ++W++  +R  Y I HW  GYF ++  G++ VRP GAD   + L ++V   R  G  LPL
Sbjct: 2   TDWSLDQARKTYSIPHWADGYFDVDQAGHMVVRPTGADGPVVSLPDVVDAARANGAKLPL 61

Query: 72  LVRFPDILQDRVRKLTGAFDANIERLEYQSRYTALYPIKVNQQEAVVENIIATENVSIGL 131
           LVRFPDIL  R+ KL  AF       EY   YTA+YPIKVNQ   V   + +      GL
Sbjct: 62  LVRFPDILGQRLGKLQAAFAQAQADWEYPGGYTAVYPIKVNQHRGVAGTLASHHGEGFGL 121

Query: 132 EAGSKPELMAVLALAPKGGTIVCNGYKDREFIKLALMGQKLGHNVFIVIEKESEVQLVIE 191
           EAGSKPELMAVLAL+  GG IVCNGYKDRE+I+LAL+G+KLG   +IVIEK SE++LV+E
Sbjct: 122 EAGSKPELMAVLALSRPGGLIVCNGYKDREYIRLALIGRKLGLQTYIVIEKPSELKLVLE 181

Query: 192 EAANVGVQPQVGLRVRLSSLASSKWADTGGEKAKFGLSAAQLLSVVERFRQAGLDQGVRL 251
           E+  + V+P +G+R+RL+SL + KW ++GG+KAKFGLS  QLL + +  R       + L
Sbjct: 182 ESKALDVKPGLGVRMRLASLGAGKWQNSGGDKAKFGLSPRQLLDLWKSLRDTEYADCLSL 241

Query: 252 LHFHMGSQIANLADYQHGFKEAIRYYGELRALGLPVDHIDVGGGLGVDYDGTHSRNASSI 311
           LHFHMGSQI+N+ D  +G +EA RYY E+  LG  + H+DVGGGLGVDY+GT SR+  SI
Sbjct: 242 LHFHMGSQISNVRDIANGMREATRYYVEMSQLGAKITHVDVGGGLGVDYEGTRSRSFCSI 301

Query: 312 NYDIDDYAGVVVGMLKEFCDAQGLPHPHIFSESGRALTAHHAVLITQVTDVERHNDD-VP 370
           NY ++ YA  +V  L + C   GL  P I +E GRA+TAHHAVLI  V++VE+  +  VP
Sbjct: 302 NYGLNSYASSIVQPLADACKEHGLKPPRIVTECGRAMTAHHAVLIANVSEVEQAMEGRVP 361

Query: 371 KIVDLDEQPEIVRWLAELLGPTDAEMVTETYWRATHYIGDAAAQYADGKISLAQKALAEQ 430
                D++P  +R L E+          E +  A H+  +  + YA G+I L Q+A  + 
Sbjct: 362 D--QHDDEPASIRHLREIHSELGQRPAIELFQEAQHFHAEGLSSYALGQIDLPQRARIDD 419

Query: 431 CYFAICRRLHNQLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWAIGQVLPILPL 490
            ++AI   +  +L   ++SHR VLDELN++L DKY  NFSVF+S+PD WAI QV PI+P+
Sbjct: 420 LFYAIAHAVRARLSFDEKSHRPVLDELNERLVDKYFVNFSVFESIPDVWAIDQVFPIVPI 479

Query: 491 HRLGEEPDRRAVLQDLTCDSDGKITQYVDEQSIETSLPVHEVKEGEDYLIGVFLVGAYQE 550
            RL E+PDRR ++ D+TCDSDG +  YV  +S+++SLP+H ++ GE Y IG F+VGAYQE
Sbjct: 480 ERLDEQPDRRGIIADMTCDSDGMVETYVGNESLDSSLPLHALRSGESYRIGFFMVGAYQE 539

Query: 551 ILGDMHNLFGDTDSVNVYQRADGGIYHAGIETHDTIEDMLRYVHLSPEELMTLYRDKVAG 610
           ILGD+HNLFGDTD+V V   A GG         DT + ML YV  S  EL   Y ++VA 
Sbjct: 540 ILGDIHNLFGDTDAVEVRAGA-GGYAITQQRRGDTTDVMLDYVGYSLAELRATYAERVAA 598

Query: 611 AKLTARERNQYLDALRLGLTRSAYLS 636
           A LTA    +  DAL  GLT   YLS
Sbjct: 599 AGLTADRAQELSDALEAGLTGYTYLS 624


Lambda     K      H
   0.319    0.137    0.401 

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: 1062
Number of extensions: 46
Number of successful extensions: 4
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: 636
Length of database: 629
Length adjustment: 38
Effective length of query: 598
Effective length of database: 591
Effective search space:   353418
Effective search space used:   353418
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 WP_057508489.1 ABB28_RS10025 (arginine decarboxylase)
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.13977.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-264  863.0   0.0   7.7e-264  862.8   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508489.1  ABB28_RS10025 arginine decarboxy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508489.1  ABB28_RS10025 arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  862.8   0.0  7.7e-264  7.7e-264       1     624 []       4     624 ..       4     624 .. 0.99

  Alignments for each domain:
  == domain 1  score: 862.8 bits;  conditional E-value: 7.7e-264
                                 TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqk 69 
                                               ws+++++k+Y+i +W++gyf+v+++G+++vrp+g++    ++l+++v++++a+g+klPllvrFpdil +
  lcl|NCBI__GCF_001431535.1:WP_057508489.1   4 WSLDQARKTYSIPHWADGYFDVDQAGHMVVRPTGAD-GPVVSLPDVVDAARANGAKLPLLVRFPDILGQ 71 
                                               8899*****************************999.899***************************** PP

                                 TIGR01273  70 rikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpEllialalaekpk 138
                                               r+ +l+aaF++a+ ++eY++ y+avyPiKvnq+r v  +l++++g+ +GLEaGsKpEl+++lal++ p+
  lcl|NCBI__GCF_001431535.1:WP_057508489.1  72 RLGKLQAAFAQAQADWEYPGGYTAVYPIKVNQHRGVAGTLASHHGEGFGLEAGSKPELMAVLALSR-PG 139
                                               ****************************************************************99.** PP

                                 TIGR01273 139 avivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwas 207
                                                +ivcnGyKDreyi+lali+rklgl+++iviek +El+lv+ee+k l vkP lG+R+rLas g+gkw++
  lcl|NCBI__GCF_001431535.1:WP_057508489.1 140 GLIVCNGYKDREYIRLALIGRKLGLQTYIVIEKPSELKLVLEESKALDVKPGLGVRMRLASLGAGKWQN 208
                                               ********************************************************************* PP

                                 TIGR01273 208 sgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvki 276
                                               sgG+k+KFGLs +q+l+++k l++++++d+l llHfH+Gsqi+n++d+++g+rEa+r+yve+++lG+ki
  lcl|NCBI__GCF_001431535.1:WP_057508489.1 209 SGGDKAKFGLSPRQLLDLWKSLRDTEYADCLSLLHFHMGSQISNVRDIANGMREATRYYVEMSQLGAKI 277
                                               ********************************************************************* PP

                                 TIGR01273 277 evvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvpePviisEsGRaitahhavlv 345
                                               ++vdvGGGLgvdY+Gt+s+s +s+nY+l+ ya+++v+ l+++c+e+g++ P+i++E+GRa+tahhavl+
  lcl|NCBI__GCF_001431535.1:WP_057508489.1 278 THVDVGGGLGVDYEGTRSRSFCSINYGLNSYASSIVQPLADACKEHGLKPPRIVTECGRAMTAHHAVLI 346
                                               ********************************************************************* PP

                                 TIGR01273 346 aevleveeeeeeeaeeileeeapeevkeleellkeideesaeelledavqlleeavelfklGkldleer 414
                                               a+v eve+  e ++++  + ++p+ +++l+e+++e+ ++ a+el+++a+++++e ++ ++lG++dl +r
  lcl|NCBI__GCF_001431535.1:WP_057508489.1 347 ANVSEVEQAMEGRVPDQHD-DEPASIRHLREIHSELGQRPAIELFQEAQHFHAEGLSSYALGQIDLPQR 414
                                               *************999776.9************************************************ PP

                                 TIGR01273 415 alaeqlalailkkvke.leakekshreildelqeklaekylvnlslFqslPDaWgidqlfPilPlerLd 482
                                               a++++l++ai ++v+  l+  ekshr++ldel+e+l++ky+vn+s+F+s+PD+W+idq+fPi+P+erLd
  lcl|NCBI__GCF_001431535.1:WP_057508489.1 415 ARIDDLFYAIAHAVRArLSFDEKSHRPVLDELNERLVDKYFVNFSVFESIPDVWAIDQVFPIVPIERLD 483
                                               ***************99**************************************************** PP

                                 TIGR01273 483 ekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvHnLFgdte 551
                                               e+pdrr++++D+tCDsDG ++ +v++++ +++lplh+l++ e+y++gff+vGAYqEiLgd+HnLFgdt+
  lcl|NCBI__GCF_001431535.1:WP_057508489.1 484 EQPDRRGIIADMTCDSDGMVETYVGNESLDSSLPLHALRSGESYRIGFFMVGAYQEILGDIHNLFGDTD 552
                                               ********************************************************************* PP

                                 TIGR01273 552 avevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkaeekkqvlelleaglsgy 620
                                               avev   + g+++++++++gdt++ +l++v y+  el+ +++++va+a l+a+++++++++leagl+gy
  lcl|NCBI__GCF_001431535.1:WP_057508489.1 553 AVEVRAGA-GGYAITQQRRGDTTDVMLDYVGYSLAELRATYAERVAAAGLTADRAQELSDALEAGLTGY 620
                                               ****8766.55********************************************************** PP

                                 TIGR01273 621 pYLs 624
                                               +YLs
  lcl|NCBI__GCF_001431535.1:WP_057508489.1 621 TYLS 624
                                               **96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (629 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: 00:00:00.04
# Mc/sec: 8.63
//
[ok]

This GapMind analysis is from Sep 24 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