Alignments for a candidate for adiA in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Bacteroides thetaiotaomicron VPI-5482

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 352921 BT3394 putative arginine decarboxylase (NCBI ptt file)

Query= BRENDA::A0A076IP90
         (630 letters)



>FitnessBrowser__Btheta:352921
          Length = 630

 Score = 1154 bits (2986), Expect = 0.0
 Identities = 567/630 (90%), Positives = 606/630 (96%)

Query: 1   MRKWRIEDSEELYNITGWGTSYFGINDKGHVVVTPRKDGVEVDLKELVDELQLRDVAAPM 60
           MRKWRIEDSEELYNITGWGTSYF IND GHVVVTPR+DGV VDLKELVDELQLRDVA+PM
Sbjct: 1   MRKWRIEDSEELYNITGWGTSYFSINDAGHVVVTPRRDGVTVDLKELVDELQLRDVASPM 60

Query: 61  LVRFPDILDNRIEKIANCFKQASDEYGYKAQNFIIYPIKVNQMRPVVEEIISHGKKFNLG 120
           L+RFPDILDNRIEK+++CFKQA++EYGYKA+NFIIYPIKVNQMRPVVEEIISHGKKFNLG
Sbjct: 61  LLRFPDILDNRIEKMSSCFKQAAEEYGYKAENFIIYPIKVNQMRPVVEEIISHGKKFNLG 120

Query: 121 LEAGSKPELHAVIAVNTDSDSLIICNGYKDESYIELALLAQKMGKRIFLVVEKMNELRLI 180
           LEAGSKPELHAVIAVNTDSDSLI+CNGYKDESYIELALLAQKMGKRIFLVVEKMNEL+LI
Sbjct: 121 LEAGSKPELHAVIAVNTDSDSLIVCNGYKDESYIELALLAQKMGKRIFLVVEKMNELKLI 180

Query: 181 AKMAKQLNVRPNIGIRIKLASSGSGKWEDSGGDASKFGLTSSELLEALDFLEKKDMKDCL 240
           AKMAKQLNV+PNIGIRIKLASSGSGKWE+SGGDASKFGLTSSELLEALDF+E K +KDCL
Sbjct: 181 AKMAKQLNVQPNIGIRIKLASSGSGKWEESGGDASKFGLTSSELLEALDFMESKGLKDCL 240

Query: 241 KLIHFHIGSQVTKIRRIKTALREASQFYVQLHVMGFNVEFVDIGGGLGVDYDGTRSANSE 300
           KLIHFHIGSQVTKIRRIKTALREASQFYVQLH MGFNVEFVDIGGGLGVDYDGTRS+NSE
Sbjct: 241 KLIHFHIGSQVTKIRRIKTALREASQFYVQLHSMGFNVEFVDIGGGLGVDYDGTRSSNSE 300

Query: 301 SSVNYSIQEYVNDSISTLVDASDKNGIPHPNIITESGRSLTAHHSVLIFEVLETATLPEM 360
            SVNYSIQEYVNDSISTLVD SDKNGIPHPNIITESGR+LTAHHSVLIFEVLETATLPE 
Sbjct: 301 GSVNYSIQEYVNDSISTLVDVSDKNGIPHPNIITESGRALTAHHSVLIFEVLETATLPEW 360

Query: 361 DEDFEVGENDHELVHELYEIWDNLNQSRMVEAWHDAQQIREEALDLFSHGIVDLKTRAQI 420
           D++ E+  + HELV ELY IWD+LNQ++M+EAWHDAQQIREEALDLFSHGIVDLKTRAQI
Sbjct: 361 DDEEEIAPDAHELVQELYSIWDSLNQNKMLEAWHDAQQIREEALDLFSHGIVDLKTRAQI 420

Query: 421 ERLYWSVTREINQIASGLKHAPDEFRKLDKLLADKYFCNFSLFQSLPDSWAIDQIFPIMP 480
           ERLYWS+TREINQIA GLKHAPDEFR L KLLADKYFCNFSLFQSLPDSWAIDQIFPIMP
Sbjct: 421 ERLYWSITREINQIAGGLKHAPDEFRGLSKLLADKYFCNFSLFQSLPDSWAIDQIFPIMP 480

Query: 481 IQRLDEKPDRNATLQDITCDSDGKIANFISTRYVSHDLPVHSLKGKDAYYIGVFLVGAYQ 540
           IQRLDEKP+R+ATLQDITCDSDGKIANFISTR V+H LPVHSLK  + YY+ VFLVGAYQ
Sbjct: 481 IQRLDEKPERSATLQDITCDSDGKIANFISTRNVAHYLPVHSLKKTEPYYLAVFLVGAYQ 540

Query: 541 EILGDMHNLFGDTNAVHVTVDDKGYSIDQVIDGETVAEVLDYVQYNPKKLVRTLETWVTK 600
           EILGDMHNLFGDTNAVHV+V++KGY+I+Q+IDGETVAEVLDYVQYNPKKLVRTLETWVTK
Sbjct: 541 EILGDMHNLFGDTNAVHVSVNEKGYNIEQIIDGETVAEVLDYVQYNPKKLVRTLETWVTK 600

Query: 601 SVKEGRISVEEGKEFLSNYRSGLYGYTYLE 630
           SVKEG+IS+EEGKEFLSNYRSGLYGYTYLE
Sbjct: 601 SVKEGKISLEEGKEFLSNYRSGLYGYTYLE 630


Lambda     K      H
   0.318    0.136    0.396 

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: 1329
Number of extensions: 37
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: 630
Length of database: 630
Length adjustment: 38
Effective length of query: 592
Effective length of database: 592
Effective search space:   350464
Effective search space used:   350464
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 352921 BT3394 (putative 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.19774.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.7e-248  810.6   0.2   5.2e-248  810.5   0.2    1.0  1  lcl|FitnessBrowser__Btheta:352921  BT3394 putative arginine decarbo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:352921  BT3394 putative arginine decarboxylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  810.5   0.2  5.2e-248  5.2e-248       1     624 []       4     630 .]       4     630 .] 0.98

  Alignments for each domain:
  == domain 1  score: 810.5 bits;  conditional E-value: 5.2e-248
                          TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslna 76 
                                        w++e+s+++Yni+gWg+ yf++n++G+v+v+p+ +    ++dl+elv++++ +++  P+l+rFpdil +ri+++ +
  lcl|FitnessBrowser__Btheta:352921   4 WRIEDSEELYNITGWGTSYFSINDAGHVVVTPRRD--GVTVDLKELVDELQLRDVASPMLLRFPDILDNRIEKMSS 77 
                                        78999***************************855..59************************************* PP

                          TIGR01273  77 aFkeaieeleYaskyqavyPiKvnqqrevveelvasg.gkslGLEaGsKpEllialalaekpkavivcnGyKDrey 151
                                         Fk+a ee++Y+++   +yPiKvnq+r vvee++++g + +lGLEaGsKpEl +++a+ + ++++ivcnGyKD+ y
  lcl|FitnessBrowser__Btheta:352921  78 CFKQAAEEYGYKAENFIIYPIKVNQMRPVVEEIISHGkKFNLGLEAGSKPELHAVIAVNTDSDSLIVCNGYKDESY 153
                                        *************************************99************************************* PP

                          TIGR01273 152 ielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvk 227
                                        ielal+a+k+g  +++v+ek++El+l+ ++ak+l+v+P++G+R++Las gsgkw++sgG+ sKFGL++s++le+++
  lcl|FitnessBrowser__Btheta:352921 154 IELALLAQKMGKRIFLVVEKMNELKLIAKMAKQLNVQPNIGIRIKLASSGSGKWEESGGDASKFGLTSSELLEALD 229
                                        **************************************************************************** PP

                          TIGR01273 228 klkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGt.ksksdlsvnY 302
                                         +++++l+d+lkl+HfH+Gsq+++i+ +k+++rEa+++yv+l+ +G ++e+vd+GGGLgvdYdGt +s+s+ svnY
  lcl|FitnessBrowser__Btheta:352921 230 FMESKGLKDCLKLIHFHIGSQVTKIRRIKTALREASQFYVQLHSMGFNVEFVDIGGGLGVDYDGTrSSNSEGSVNY 305
                                        *****************************************************************6777899**** PP

                          TIGR01273 303 sleeyaaavvaalkevceekgvpePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevkeleell 378
                                        s++ey ++ +++l +v +++g p+P+ii+EsGRa+tahh+vl++evle+ + +e ++ee ++ +a e+v+el  + 
  lcl|FitnessBrowser__Btheta:352921 306 SIQEYVNDSISTLVDVSDKNGIPHPNIITESGRALTAHHSVLIFEVLETATLPEWDDEEEIAPDAHELVQELYSIW 381
                                        ****************************************************99997766776************* PP

                          TIGR01273 379 keideesaeelledavqlleeavelfklGkldleeralaeqlalailkkvkeleakekshreildelqeklaekyl 454
                                         +++++++ e ++da+q+ eea+ lf++G++dl++ra++e+l+ +i+++++++    k+  ++ + l + la+ky+
  lcl|FitnessBrowser__Btheta:352921 382 DSLNQNKMLEAWHDAQQIREEALDLFSHGIVDLKTRAQIERLYWSITREINQIAGGLKHAPDEFRGLSKLLADKYF 457
                                        **************************************************************************** PP

                          TIGR01273 455 vnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgf 530
                                        +n+slFqslPD+W+idq+fPi+P++rLdekp+r+a+l+D+tCDsDGki++f+ +++ +++lp+h+l+k+e+y+l++
  lcl|FitnessBrowser__Btheta:352921 458 CNFSLFQSLPDSWAIDQIFPIMPIQRLDEKPERSATLQDITCDSDGKIANFISTRNVAHYLPVHSLKKTEPYYLAV 533
                                        **************************************************************************** PP

                          TIGR01273 531 flvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqk....vaeaklk 602
                                        flvGAYqEiLgd+HnLFgdt+av+v v+ekg +++e+i  g+tv++vl++vqy+p++l ++l++     v+e k++
  lcl|FitnessBrowser__Btheta:352921 534 FLVGAYQEILGDMHNLFGDTNAVHVSVNEKG-YNIEQIIDGETVAEVLDYVQYNPKKLVRTLETWvtksVKEGKIS 608
                                        ******************************9.**************************9999877666789999** PP

                          TIGR01273 603 aeekkqvlelleaglsgypYLs 624
                                         ee k++l+ +++gl+gy+YL+
  lcl|FitnessBrowser__Btheta:352921 609 LEEGKEFLSNYRSGLYGYTYLE 630
                                        ********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (630 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.61
//
[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)
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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