Alignments for a candidate for adiA in Caminibacter mediatlanticus TB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Caminibacter mediatlanticus TB-2

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_007474095.1 CMTB2_RS03735 biosynthetic arginine decarboxylase

Query= BRENDA::Q0PAC6
         (611 letters)



>NCBI__GCF_000170735.1:WP_007474095.1
          Length = 608

 Score =  780 bits (2013), Expect = 0.0
 Identities = 375/612 (61%), Positives = 500/612 (81%), Gaps = 10/612 (1%)

Query: 2   MDYGIDIWGNENFIIKNGKVCINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIEN 61
           M+YGIDIWG  NF I+NGK+ +N+  +PA+IDI+KE+ + G++GP+LLRFPHLI+KQI +
Sbjct: 1   MNYGIDIWGGNNFFIENGKLKVNFGNQPALIDIIKEIEERGFQGPILLRFPHLIRKQINS 60

Query: 62  IYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSKAELLLAMA 121
           +Y  FNKA KEF YKG F+AV+PLKVNQ+P FVK L+K+   +NYGLEAGSKAEL+LAMA
Sbjct: 61  LYSAFNKAIKEFNYKGKFHAVFPLKVNQFPTFVKPLIKIANKFNYGLEAGSKAELILAMA 120

Query: 122 YNNEGAPITVNGFKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIG 181
           YNN+ APIT+NGFKD+++I + FIA  MG+++T+TIEGLNEL +II+++KE  K   NIG
Sbjct: 121 YNNKNAPITINGFKDKDMIRLAFIAGFMGYDVTITIEGLNELNSIIEVSKEYEKIPVNIG 180

Query: 182 LRVRLHSAGVGIWAKSGGINSKFGLTSTELIEAVNLLKENKLLEQFTMIHFHLGSQITEI 241
           +R+RLH++GVGIWAKSGGI SKFGL+STE+IEA+++LK+ K+L++  MIHFH+GSQI +I
Sbjct: 181 IRIRLHTSGVGIWAKSGGIESKFGLSSTEIIEAIDILKKEKMLDKLKMIHFHIGSQINDI 240

Query: 242 HPLKKALNEAGNIYTELRKMGAKNLKAINLGGGLAVEYSQFKNEKSRNYTLREYANDVVF 301
            PLKKA+ E+GNIY +LRKMGAKNL AIN+GGGLA+EYSQ++ ++ +NY++ E++NDVV+
Sbjct: 241 SPLKKAIRESGNIYADLRKMGAKNLSAINIGGGLAIEYSQWEEKRDKNYSIEEFSNDVVY 300

Query: 302 ILKNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDE 361
           +LK I+++K+   PDIF ESGRF+A+   +LIAPV+ELFSQEY E  L LK +NP L++E
Sbjct: 301 LLKEISQKKEVPMPDIFTESGRFIASPSTILIAPVIELFSQEYHEKNLKLKDKNPDLVEE 360

Query: 362 LYDLYKSIKPSNALEYLHDSIDHLESILTLFDLGYVDLQDRSNAEILTHLITKKAI---L 418
           LYDLYK+I  +N +EY HD++DH ES+LTLFDLG +DL DRSN+EIL +L+ KKAI    
Sbjct: 361 LYDLYKTINENNYIEYFHDALDHFESLLTLFDLGIIDLIDRSNSEILVNLMIKKAITYAT 420

Query: 419 LLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGLEQNFPIMPLDRLDEEPTRSASI 478
           L G K    DL +I +++QE+YL NFS+FQS+PDFWGL Q FPIMPL +L+  PTRSA+I
Sbjct: 421 LKGFKNK--DLKSINEKIQEKYLANFSIFQSLPDFWGLGQRFPIMPLTKLNITPTRSATI 478

Query: 479 WDITCDSDGEISYSKDKPLFLHDVDVEKENYFLGFFLVGAYQEVLGMKHNLFTHPTEAII 538
           WDITCDSDGEI +SK+ PL+LHDVD+EKE+Y+LGFFLVGAYQE+LGMKHNLF++  EAII
Sbjct: 479 WDITCDSDGEIPFSKEYPLYLHDVDLEKEDYYLGFFLVGAYQEILGMKHNLFSYTNEAII 538

Query: 539 SINEKG-YEVEGIIEAQSILDTLEDLDYDIHAIMDILNERISNSKLVND-KQKKHILGEL 596
           + + +G YE+E +   Q I + L DLDYDI  I  +L  ++   +++ND +++K ILGEL
Sbjct: 539 NFDIEGNYEIEFLEPTQKIREILIDLDYDIDEIERLLKNKL---EIINDEEERKEILGEL 595

Query: 597 YLFLNDNGYLKS 608
           +L LND  YLK+
Sbjct: 596 FLLLNDMIYLKN 607


Lambda     K      H
   0.318    0.139    0.400 

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: 1343
Number of extensions: 69
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: 611
Length of database: 608
Length adjustment: 37
Effective length of query: 574
Effective length of database: 571
Effective search space:   327754
Effective search space used:   327754
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: 53 (25.0 bits)

Align candidate WP_007474095.1 CMTB2_RS03735 (biosynthetic 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.6281.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-205  668.5   0.5   5.7e-205  668.3   0.5    1.0  1  lcl|NCBI__GCF_000170735.1:WP_007474095.1  CMTB2_RS03735 biosynthetic argin


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000170735.1:WP_007474095.1  CMTB2_RS03735 biosynthetic arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  668.3   0.5  5.7e-205  5.7e-205       9     624 .]       2     606 ..       1     606 [. 0.97

  Alignments for each domain:
  == domain 1  score: 668.3 bits;  conditional E-value: 5.7e-205
                                 TIGR01273   9 vYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslnaa 77 
                                                Y+i+ Wg + f +++ G+++v+       ++  l +++k++e++g+++P+l+rFp++++k+i+sl +a
  lcl|NCBI__GCF_000170735.1:WP_007474095.1   2 NYGIDIWGGNNFFIEN-GKLKVNFG-----NQPALIDIIKEIEERGFQGPILLRFPHLIRKQINSLYSA 64 
                                               59************99.******97.....4579*********************************** PP

                                 TIGR01273  78 FkeaieeleYaskyqavyPiKvnqqrevveelvasg.gkslGLEaGsKpEllialalaekpkavivcnG 145
                                               F++ai+e +Y++k++av+P+Kvnq  ++v+ l++ + + ++GLEaGsK+El++a+a+ + ++a+i++nG
  lcl|NCBI__GCF_000170735.1:WP_007474095.1  65 FNKAIKEFNYKGKFHAVFPLKVNQFPTFVKPLIKIAnKFNYGLEAGSKAELILAMAYNN-KNAPITING 132
                                               ***********************************999********************9.8999***** PP

                                 TIGR01273 146 yKDreyielaliarklglkvviviekleEldlvieeakklgvkP.klGlRvrLaskgsgkwassgGeks 213
                                               +KD+++i+la+ia  +g++v+i+ie l+El+ +ie++k+ +  P ++G+R+rL++ g+g wa+sgG +s
  lcl|NCBI__GCF_000170735.1:WP_007474095.1 133 FKDKDMIRLAFIAGFMGYDVTITIEGLNELNSIIEVSKEYEKIPvNIGIRIRLHTSGVGIWAKSGGIES 201
                                               ***************************************8777747*********************** PP

                                 TIGR01273 214 KFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvk.ievvdv 281
                                               KFGLs+++++e+++ lk+e++ld+lk++HfH+Gsqi +i+ +kk++rE+ ++y++lrk+G+k ++ +++
  lcl|NCBI__GCF_000170735.1:WP_007474095.1 202 KFGLSSTEIIEAIDILKKEKMLDKLKMIHFHIGSQINDISPLKKAIRESGNIYADLRKMGAKnLSAINI 270
                                               ********************************************************************* PP

                                 TIGR01273 282 GGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvpePviisEsGRaitahhavlvaevle 350
                                               GGGL+++Y   + +++ + nYs+ee++++vv+ lke+ ++k+vp P+i++EsGR i++  ++l+a v+e
  lcl|NCBI__GCF_000170735.1:WP_007474095.1 271 GGGLAIEYS--QWEEKRDKNYSIEEFSNDVVYLLKEISQKKEVPMPDIFTESGRFIASPSTILIAPVIE 337
                                               ********9..999999**************************************************** PP

                                 TIGR01273 351 veeeeeeeaeeileeeapeevkeleellkeideesaeelledavqlleeavelfklGkldleeralaeq 419
                                               + ++e++e++  l++++p +v+el +l+k+i+e++ +e+++da +++e++++lf+lG++dl +r++ e 
  lcl|NCBI__GCF_000170735.1:WP_007474095.1 338 LFSQEYHEKNLKLKDKNPDLVEELYDLYKTINENNYIEYFHDALDHFESLLTLFDLGIIDLIDRSNSEI 406
                                               *******97777888****************************************************** PP

                                 TIGR01273 420 lalailkkvkeleakekshreildelqeklaekylvnlslFqslPDaWgidqlfPilPlerLdekpdrr 488
                                               l++ ++kk+    + +  +++ l+ ++ek++ekyl+n+s+FqslPD+Wg++q fPi+Pl +L+ +p+r+
  lcl|NCBI__GCF_000170735.1:WP_007474095.1 407 LVNLMIKKAITYATLKGFKNKDLKSINEKIQEKYLANFSIFQSLPDFWGLGQRFPIMPLTKLNITPTRS 475
                                               *****99999877778888899999******************************************** PP

                                 TIGR01273 489 avllDltCDsDGkikkfveeqgiektlplheldkdee.yllgfflvGAYqEiLgdvHnLFgdteavevv 556
                                               a+++D+tCDsDG+i       ++e  l lh++d ++e y+lgfflvGAYqEiLg++HnLF+ t+++ ++
  lcl|NCBI__GCF_000170735.1:WP_007474095.1 476 ATIWDITCDSDGEIP-----FSKEYPLYLHDVDLEKEdYYLGFFLVGAYQEILGMKHNLFSYTNEAIIN 539
                                               **************9.....566899*******87666******************************* PP

                                 TIGR01273 557 vkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkaeekkqvlelleaglsgypYLs 624
                                               ++ +g++e+e  e  +++ ++l +++yd +e+++ lk+k +  + ++ee+k++l +l   l+++ YL+
  lcl|NCBI__GCF_000170735.1:WP_007474095.1 540 FDIEGNYEIEFLEPTQKIREILIDLDYDIDEIERLLKNKLEIIN-DEEERKEILGELFLLLNDMIYLK 606
                                               ***************************************77754.88999****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (608 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: 11.67
//
[ok]

This GapMind analysis is from Sep 24 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