Alignments for a candidate for adiA in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Desulfovibrio vulgaris Miyazaki F

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 8500795 DvMF_1536 arginine decarboxylase (RefSeq)

Query= BRENDA::P74576
         (695 letters)



>FitnessBrowser__Miya:8500795
          Length = 645

 Score =  541 bits (1395), Expect = e-158
 Identities = 274/649 (42%), Positives = 420/649 (64%), Gaps = 22/649 (3%)

Query: 43  RRWTIDDSENLYRITGWGEPYFSINAAGHVTVSPQADHGG-ALDLYELVKGLRQRNIGLP 101
           ++W+++DS  LY I  WG  YF +  +G V V P  D+ G A+ + E+++G+R+R   +P
Sbjct: 14  QQWSVEDSAELYGIRNWGAGYFDVAQSGDVVVYPFGDNRGPAVSIPEIIRGMRERGYDMP 73

Query: 102 LLLRFSDILADRINRLNAAFARGIARYRYPNTYRGVYPIKCNQHRHIVESLVRYGTPYNF 161
           +LLR  +IL  +I  L+ +F + I    Y   YRG++PIK NQ + +VE + ++G+ Y+ 
Sbjct: 74  VLLRIENILDSQITSLHQSFRKAIGSLGYKGEYRGIFPIKVNQQQQVVEKIAQFGSRYHH 133

Query: 162 GLEAGSKPELMIALAMLQPQENPEPDQQNQPLLICNGYKDREYIETALLARRLGHRPIIV 221
           GLE GSK EL+ A++ L+  E           L+CNGYKD E+I+  L A R+G++   V
Sbjct: 134 GLEVGSKAELIAAVSQLRDHE---------ACLVCNGYKDEEFIDLGLHAVRMGYKCFFV 184

Query: 222 VEQVAEVALAIEISSNLGIKPILGVRAKLSTQGMGRWGISTGDRAKFGLTIPEMLTAIEQ 281
           +E  +E+ L +E S  LG++P++GVRAKLS +  G W  S G+R+ FGLT  +++  ++Q
Sbjct: 185 LEMASELPLILERSKCLGVRPLIGVRAKLSVKAGGHWTDSGGERSTFGLTTAQIVDVVDQ 244

Query: 282 LRRADMLDSLQLLHFHIGSQISSISVIKEAMTEASQIFVQLAKLGANMRYLDVGGGLGVD 341
           L+  DMLD  QLLH+H+GSQ+ +I  I+ A+ EA +I+  L   GA M YLD+GGGL VD
Sbjct: 245 LKDHDMLDCFQLLHYHLGSQVPNIRDIRAAVMEACRIYGGLVAEGAAMGYLDLGGGLAVD 304

Query: 342 YDGSKTNFYASKNYNIQNYVNDVISAVQDACVAAEVPCPVLISESGRAIASHQSVLIFDV 401
           YDGS TN+ +S+NY++  Y  D+I AV +      +  P +++ESGRA  ++ S+L+F++
Sbjct: 305 YDGSHTNYVSSRNYSLDEYCADIIEAVMNILDEEGIAHPHIVTESGRATVAYYSMLLFNI 364

Query: 402 VATNDIN-PPLPKVKGKD-HAILRNLMETWETITVDNYQEAYHDVEQFKTEAISLFNFGY 459
           +  + +    LP +   D    +RN+ E    +T+ N QE Y+D   ++ E    F  G 
Sbjct: 365 LDVSRVEIGNLPDILPDDCPEPVRNMREALAGLTLRNLQECYNDAVYYRDEVRQQFLTGR 424

Query: 460 LGLKERAKAEELYWACCRKILQICRQQEYVPDDLENLEVNLASIYYANMSVFQSAPDSWA 519
           + L+ER   E  +WA  ++I Q  ++ ++VP DL  ++V LA IYY N SVFQS PDSWA
Sbjct: 425 ITLRERTLGERYFWAIMKRIAQEKQKLKHVPKDLAEIDVALADIYYGNFSVFQSLPDSWA 484

Query: 520 IDQLFPIMPIHRLDEEPTQRGILADITCDSDGKIDQFIDLRDVKSVLELHPLIEVHQPGT 579
           IDQLFP++P+HRL+E P+++GIL+DITCDSDG+ID FID + VK  L+LHPL +      
Sbjct: 485 IDQLFPVVPLHRLNELPSRQGILSDITCDSDGRIDHFIDPQGVKGTLDLHPLKD------ 538

Query: 580 PPRVEPYYLGMFLVGAYQEIMGNLHNLFGDINVVHIQMNPKG-YQIEHLVRGDTIAEVLG 638
               E YYLG+FLVGAYQE +G+LHNL GD NVV ++++  G Y+    +RGD++A++L 
Sbjct: 539 ---GEEYYLGVFLVGAYQETLGDLHNLLGDTNVVSVRVHEDGSYEFVRELRGDSVADILS 595

Query: 639 YVQYDPEDLLENMRRYCEQAMEDKRMSLEEAQLLLENYERSLLQYTYLK 687
           YV+YDP  +++++R   EQA+ + R++  +   +++ YE  L  YTY +
Sbjct: 596 YVEYDPRRIIDDIREAAEQAVREGRITPSDRYRVMQAYEDGLRGYTYFE 644


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: 1057
Number of extensions: 41
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: 645
Length adjustment: 39
Effective length of query: 656
Effective length of database: 606
Effective search space:   397536
Effective search space used:   397536
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 8500795 DvMF_1536 (arginine decarboxylase (RefSeq))
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.20899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.7e-222  724.2   0.0   7.6e-222  724.1   0.0    1.0  1  lcl|FitnessBrowser__Miya:8500795  DvMF_1536 arginine decarboxylase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8500795  DvMF_1536 arginine decarboxylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  724.1   0.0  7.6e-222  7.6e-222       1     623 [.      16     643 ..      16     644 .. 0.99

  Alignments for each domain:
  == domain 1  score: 724.1 bits;  conditional E-value: 7.6e-222
                         TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslnaa 77 
                                       ws+e+sa++Y+i++Wgagyf+v ++G+v+v p g++    ++++e++  ++++g+ +P+l+r  +il ++i+sl++ 
  lcl|FitnessBrowser__Miya:8500795  16 WSVEDSAELYGIRNWGAGYFDVAQSGDVVVYPFGDNRGPAVSIPEIIRGMRERGYDMPVLLRIENILDSQITSLHQS 92 
                                       8999************************************************************************* PP

                         TIGR01273  78 FkeaieeleYaskyqavyPiKvnqqrevveelvasg.gkslGLEaGsKpEllialalaekpkavivcnGyKDreyie 153
                                       F++ai +l+Y+++y++++PiKvnqq++vve+++++g +++ GLE+GsK+El++a++ ++ ++a++vcnGyKD+e+i+
  lcl|FitnessBrowser__Miya:8500795  93 FRKAIGSLGYKGEYRGIFPIKVNQQQQVVEKIAQFGsRYHHGLEVGSKAELIAAVSQLRDHEACLVCNGYKDEEFID 169
                                       ************************************99*************************************** PP

                         TIGR01273 154 laliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvkklk 230
                                       l+l a ++g+k + v+e+ +El l++e +k lgv+P +G+R++L+ k+ g+w++sgGe+s FGL+++q+++vv++lk
  lcl|FitnessBrowser__Miya:8500795 170 LGLHAVRMGYKCFFVLEMASELPLILERSKCLGVRPLIGVRAKLSVKAGGHWTDSGGERSTFGLTTAQIVDVVDQLK 246
                                       ***************************************************************************** PP

                         TIGR01273 231 eedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsleey 307
                                       ++d+ld+++llH+HlGsq++ni+d++ +v Ea r+y  l+  G+++ ++d+GGGL+vdYdG++ ++ +s nYsl+ey
  lcl|FitnessBrowser__Miya:8500795 247 DHDMLDCFQLLHYHLGSQVPNIRDIRAAVMEACRIYGGLVAEGAAMGYLDLGGGLAVDYDGSHTNYVSSRNYSLDEY 323
                                       ***************************************************************************** PP

                         TIGR01273 308 aaavvaalkevceekgvpePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevkeleellkeidee 384
                                        a+++ a+ ++ +e+g  +P+i++EsGRa++a++++l++++l+v++ e  + ++il ++ pe v++++e l+ ++ +
  lcl|FitnessBrowser__Miya:8500795 324 CADIIEAVMNILDEEGIAHPHIVTESGRATVAYYSMLLFNILDVSRVEIGNLPDILPDDCPEPVRNMREALAGLTLR 400
                                       ***************************************************************************** PP

                         TIGR01273 385 saeelledavqlleeavelfklGkldleeralaeqlalailkkvkeleakekshreildelqeklaekylvnlslFq 461
                                       +++e+++dav + +e+ ++f +G+++l+er+l e+ + ai+k++ + ++k k+  + l e++  la+ y+ n+s+Fq
  lcl|FitnessBrowser__Miya:8500795 401 NLQECYNDAVYYRDEVRQQFLTGRITLRERTLGERYFWAIMKRIAQEKQKLKHVPKDLAEIDVALADIYYGNFSVFQ 477
                                       **********************************************99999999*********************** PP

                         TIGR01273 462 slPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqE 538
                                       slPD+W+idqlfP++Pl+rL+e p r+++l+D+tCDsDG+i++f++ qg + tl lh l+  eey+lg+flvGAYqE
  lcl|FitnessBrowser__Miya:8500795 478 SLPDSWAIDQLFPVVPLHRLNELPSRQGILSDITCDSDGRIDHFIDPQGVKGTLDLHPLKDGEEYYLGVFLVGAYQE 554
                                       ***************************************************************************** PP

                         TIGR01273 539 iLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqk....vaeaklkaeekkqvle 611
                                        Lgd HnL gdt++v+v v+e+g++e  +  +gd+v+d+l++v+ydp ++ +++++     v+e +++ +++ +v++
  lcl|FitnessBrowser__Miya:8500795 555 TLGDLHNLLGDTNVVSVRVHEDGSYEFVRELRGDSVADILSYVEYDPRRIIDDIREAaeqaVREGRITPSDRYRVMQ 631
                                       ****************************************************9999877667778899********* PP

                         TIGR01273 612 lleaglsgypYL 623
                                       ++e gl+gy+Y 
  lcl|FitnessBrowser__Miya:8500795 632 AYEDGLRGYTYF 643
                                       ***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (645 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: 7.88
//
[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