Alignments for a candidate for adiA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Desulfovibrio vulgaris Hildenborough

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 209353 DVU0417 arginine decarboxylase

Query= BRENDA::P74576
         (695 letters)



>MicrobesOnline__882:209353
          Length = 659

 Score =  534 bits (1376), Expect = e-156
 Identities = 273/649 (42%), Positives = 412/649 (63%), Gaps = 22/649 (3%)

Query: 43  RRWTIDDSENLYRITGWGEPYFSINAAGHVTVSPQA-DHGGALDLYELVKGLRQRNIGLP 101
           ++W ++DS  LY I  WG  YF +   G V V P   + G A+ + E++ G+R+R   +P
Sbjct: 28  QQWGVEDSAELYGIRNWGAGYFDVAQNGDVVVYPFGHNRGPAVSIPEIIGGMRERGYDMP 87

Query: 102 LLLRFSDILADRINRLNAAFARGIARYRYPNTYRGVYPIKCNQHRHIVESLVRYGTPYNF 161
           +LLR  +IL  +I  L+ +F   I    Y   YRG++PIK NQ + +VE + ++G+ Y+ 
Sbjct: 88  VLLRIENILDSQITSLHTSFRNAIGSLGYKGEYRGIFPIKVNQQQQVVEKIAQFGSHYHH 147

Query: 162 GLEAGSKPELMIALAMLQPQENPEPDQQNQPLLICNGYKDREYIETALLARRLGHRPIIV 221
           GLE GSK EL+ A++ L+ +E           L+CNGYKD E+I+  L A RLG   I V
Sbjct: 148 GLEVGSKAELIAAVSQLRDRE---------ACLVCNGYKDEEFIDLGLHAVRLGFMCIFV 198

Query: 222 VEQVAEVALAIEISSNLGIKPILGVRAKLSTQGMGRWGISTGDRAKFGLTIPEMLTAIEQ 281
           +E   E+ L +E    LG+KPI+GVRAKLS +  G W  S G+R+ FGLT  +++  +++
Sbjct: 199 LEMPGELDLILERGEALGVKPIIGVRAKLSVKAGGHWTDSGGERSTFGLTTSQIVDVVDR 258

Query: 282 LRRADMLDSLQLLHFHIGSQISSISVIKEAMTEASQIFVQLAKLGANMRYLDVGGGLGVD 341
           L+   MLD  +LLH+H+GSQ+ +I  I+ A+ EA +I+  L + GA M +LD+GGGL VD
Sbjct: 259 LKEKGMLDCFKLLHYHLGSQVPNIRDIRAAVMEACRIYAGLVQEGAAMGFLDLGGGLAVD 318

Query: 342 YDGSKTNFYASKNYNIQNYVNDVISAVQDACVAAEVPCPVLISESGRAIASHQSVLIFDV 401
           YDGS TNF +S+NY +  Y  D++ AV        +P P +++ESGRA  ++ S+L+F++
Sbjct: 319 YDGSHTNFVSSRNYTLDEYCADIVEAVMTTLDEQNIPHPHIVTESGRATVAYYSMLLFNI 378

Query: 402 VATNDIN-PPLPKVKGKD-HAILRNLMETWETITVDNYQEAYHDVEQFKTEAISLFNFGY 459
           +  + +    LP    +D    +RN+ E    +T+ N QE Y+D   ++     LF  G 
Sbjct: 379 LDVSRVEIGNLPDALPEDTPEPVRNMREVLAGMTLRNLQECYNDALYYRDAVRQLFLTGQ 438

Query: 460 LGLKERAKAEELYWACCRKILQICRQQEYVPDDLENLEVNLASIYYANMSVFQSAPDSWA 519
           + L++R  +E L+WA  ++I Q  ++ ++VP DL  ++V LA IYY N SVFQS PDSWA
Sbjct: 439 VTLRQRTLSERLFWAIMKRIAQEKQKLKHVPKDLAEIDVALADIYYGNFSVFQSLPDSWA 498

Query: 520 IDQLFPIMPIHRLDEEPTQRGILADITCDSDGKIDQFIDLRDVKSVLELHPLIEVHQPGT 579
           IDQLFP+MP+HRL E P+++GIL+DITCDSDG+ID FID + +K  L+LHPL +      
Sbjct: 499 IDQLFPVMPVHRLQELPSRQGILSDITCDSDGRIDHFIDPQGMKGTLDLHPLRD------ 552

Query: 580 PPRVEPYYLGMFLVGAYQEIMGNLHNLFGDINVVHIQMNPKG-YQIEHLVRGDTIAEVLG 638
               E YYLG+FLVGAYQE +G+LHNL GD NVV ++++  G Y+    +RGD++A++L 
Sbjct: 553 ---GEEYYLGVFLVGAYQETLGDLHNLLGDTNVVSVRVHEDGTYEFVREIRGDSVADILS 609

Query: 639 YVQYDPEDLLENMRRYCEQAMEDKRMSLEEAQLLLENYERSLLQYTYLK 687
           YV+YDP  + E++R   E+A+ + R++  +   +++ YE  L  YTY +
Sbjct: 610 YVEYDPRRIYEDIRELAERAVREGRITASDRFRVMQAYEDGLRGYTYFE 658


Lambda     K      H
   0.319    0.137    0.402 

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: 1027
Number of extensions: 36
Number of successful extensions: 6
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: 695
Length of database: 659
Length adjustment: 39
Effective length of query: 656
Effective length of database: 620
Effective search space:   406720
Effective search space used:   406720
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 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate 209353 DVU0417 (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.11302.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     4e-221  721.7   0.0   4.6e-221  721.5   0.0    1.0  1  lcl|MicrobesOnline__882:209353  DVU0417 arginine decarboxylase


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209353  DVU0417 arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  721.5   0.0  4.6e-221  4.6e-221       1     623 [.      30     657 ..      30     658 .. 0.99

  Alignments for each domain:
  == domain 1  score: 721.5 bits;  conditional E-value: 4.6e-221
                       TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslnaaFk 79 
                                     w +e+sa++Y+i++Wgagyf+v ++G+v+v p g++    ++++e++  ++++g+ +P+l+r  +il ++i+sl++ F+
  lcl|MicrobesOnline__882:209353  30 WGVEDSAELYGIRNWGAGYFDVAQNGDVVVYPFGHNRGPAVSIPEIIGGMRERGYDMPVLLRIENILDSQITSLHTSFR 108
                                     667899************************************************************************* PP

                       TIGR01273  80 eaieeleYaskyqavyPiKvnqqrevveelvasg.gkslGLEaGsKpEllialalaekpkavivcnGyKDreyielali 157
                                     +ai +l+Y+++y++++PiKvnqq++vve+++++g +++ GLE+GsK+El++a++ ++  +a++vcnGyKD+e+i+l+l 
  lcl|MicrobesOnline__882:209353 109 NAIGSLGYKGEYRGIFPIKVNQQQQVVEKIAQFGsHYHHGLEVGSKAELIAAVSQLRDREACLVCNGYKDEEFIDLGLH 187
                                     **********************************99******************************************* PP

                       TIGR01273 158 arklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvkklkeedlld 236
                                     a +lg+  + v+e+  Eldl++e  + lgvkP +G+R++L+ k+ g+w++sgGe+s FGL++sq+++vv++lke+++ld
  lcl|MicrobesOnline__882:209353 188 AVRLGFMCIFVLEMPGELDLILERGEALGVKPIIGVRAKLSVKAGGHWTDSGGERSTFGLTTSQIVDVVDRLKEKGMLD 266
                                     ******************************************************************************* PP

                       TIGR01273 237 slkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaal 315
                                     ++kllH+HlGsq++ni+d++ +v Ea r+y+ l++ G+++ ++d+GGGL+vdYdG++ +  +s nY+l+ey a++v a+
  lcl|MicrobesOnline__882:209353 267 CFKLLHYHLGSQVPNIRDIRAAVMEACRIYAGLVQEGAAMGFLDLGGGLAVDYDGSHTNFVSSRNYTLDEYCADIVEAV 345
                                     ******************************************************************************* PP

                       TIGR01273 316 kevceekgvpePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevkeleellkeideesaeelledav 394
                                      ++ +e++ p+P+i++EsGRa++a++++l++++l+v++ e  + ++ l e++pe v++++e+l+ ++ ++++e+++da 
  lcl|MicrobesOnline__882:209353 346 MTTLDEQNIPHPHIVTESGRATVAYYSMLLFNILDVSRVEIGNLPDALPEDTPEPVRNMREVLAGMTLRNLQECYNDAL 424
                                     ******************************************************************************* PP

                       TIGR01273 395 qlleeavelfklGkldleeralaeqlalailkkvkeleakekshreildelqeklaekylvnlslFqslPDaWgidqlf 473
                                      + + + +lf +G+++l++r+l e+l+ ai+k++ + ++k k+  + l e++  la+ y+ n+s+FqslPD+W+idqlf
  lcl|MicrobesOnline__882:209353 425 YYRDAVRQLFLTGQVTLRQRTLSERLFWAIMKRIAQEKQKLKHVPKDLAEIDVALADIYYGNFSVFQSLPDSWAIDQLF 503
                                     ************************************99999999*********************************** PP

                       TIGR01273 474 PilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvHnLFgdtea 552
                                     P++P++rL+e p r+++l+D+tCDsDG+i++f++ qg++ tl lh l+  eey+lg+flvGAYqE Lgd HnL gdt++
  lcl|MicrobesOnline__882:209353 504 PVMPVHRLQELPSRQGILSDITCDSDGRIDHFIDPQGMKGTLDLHPLRDGEEYYLGVFLVGAYQETLGDLHNLLGDTNV 582
                                     ******************************************************************************* PP

                       TIGR01273 553 vevvvkekgeveveaieegdtvedvlkavqydpeellkalkqk....vaeaklkaeekkqvlelleaglsgypYL 623
                                     v+v v+e+g +e  +  +gd+v+d+l++v+ydp ++++++++     v+e +++a+++ +v++++e gl+gy+Y 
  lcl|MicrobesOnline__882:209353 583 VSVRVHEDGTYEFVREIRGDSVADILSYVEYDPRRIYEDIRELaeraVREGRITASDRFRVMQAYEDGLRGYTYF 657
                                     *****************************************99777778888**********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (659 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.77
//
[ok]

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

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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