Alignments for a candidate for adiA in Methylococcus capsulatus Bath

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Methylococcus capsulatus Bath

Align Biosynthetic arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_010961291.1 MCA_RS10020 biosynthetic arginine decarboxylase

Query= reanno::psRCH2:GFF3302
         (637 letters)



>NCBI__GCF_000008325.1:WP_010961291.1
          Length = 625

 Score =  635 bits (1638), Expect = 0.0
 Identities = 329/626 (52%), Positives = 425/626 (67%), Gaps = 8/626 (1%)

Query: 12  SQWTAADSRSIYGIRHWGAGYFAISDEGNVEVRPQGPSGEP-IEFNGLIEQLREAGLSLP 70
           + WT +D+R  Y I HW  GYF I+ EG V V PQ  S E  +    +   +R  GLSLP
Sbjct: 4   ANWTLSDARDTYAIEHWSDGYFNIAPEGEVVVCPQRGSVEGGVSIAAIARGVRAEGLSLP 63

Query: 71  LLVRFPGILQDRVRRLTGAFDANIERMEYAGKYTALYPIKVNQQEAVVENIIATQNVSIG 130
           +L+RFP IL DRVR LT AF        Y   YT +YPIKVNQQ  V+ENI+    V  G
Sbjct: 64  VLMRFPHILHDRVRLLTSAFGKARAAYHYGAGYTPVYPIKVNQQRNVIENILRAGGV--G 121

Query: 131 LEAGSKPELMAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHKVFIVIEKESEVGLVI 190
           LEAGSK EL+A+LALA + GTI+CNGYKDR +IRLAL+G +LG +VFIV+EK SE+ LV+
Sbjct: 122 LEAGSKSELLAILALA-ESGTIICNGYKDRAYIRLALIGSRLGLRVFIVVEKLSELELVV 180

Query: 191 EEANELKLTPQVGLRVRLSSLASSKWADTGGERSKFGLSAAQLLSVIERFRAAEMDQGIR 250
            E+  L + PQ+G+R+RLSS+++ KW ++GGE+SKFGL A ++L  ++R   A     +R
Sbjct: 181 SESEALGIAPQLGVRIRLSSISAGKWQNSGGEKSKFGLHAGEILKFLKRLERAGGLGWVR 240

Query: 251 LLHFHMGSQIANLADYRQGFREAIRYYAELRALNLPVDYIDVGGGLGVDYDGTHSRNASS 310
           L+HFHMGSQ+AN+ D +   REA RYYAELR L  PVD++DVGGGLG+DY+GTHS +  S
Sbjct: 241 LMHFHMGSQVANINDVKTALREASRYYAELRRLGAPVDHVDVGGGLGIDYEGTHSVSDCS 300

Query: 311 INYDIDEYAGTVVGMLKEFCEAQGLPHPNIFSESGRAMTAHHAVLVMQVTDVERHN-DEL 369
           INY +DEYA ++V    E C  QGLP P++ +E+GRAM+AHHAVLV  V D+E    D  
Sbjct: 301 INYSVDEYAHSIVRAFSELCAEQGLPQPDLITEAGRAMSAHHAVLVTNVVDIEAATYDAS 360

Query: 370 PVIENYDELPEIVQSLADLLGPTDPEMVTETYWRATHYMSESSAQYASGKLTLAQKALAE 429
           PV  +   + + ++ L DLL   D E V   Y  A   ++E+   Y  GK+ L Q A AE
Sbjct: 361 PVSAS---VAQPLKDLEDLLRRVDSESVLGIYHDAEFDLAETRTMYVQGKIGLDQLAEAE 417

Query: 430 QSYFAICRRLYNQLKARQRSHRAVLDELNDKLADKYICNFSVFQSLPDTWAIDQILPIVP 489
           + +  +CR +  +L  R R+HRAVLDELN++LADK  CNFSVFQS+PD WAIDQI P++P
Sbjct: 418 RLHATLCREVQQRLDIRLRAHRAVLDELNERLADKLFCNFSVFQSIPDAWAIDQIFPVMP 477

Query: 490 LQRLSEEPVRRAVLQDLTCDSDGKIKHYVDEQSIESSMPVHEVAPGEEYFLGVFLVGAYQ 549
           LQRL EEP RRAV+QD+TCDSDG+I  Y+D QSIE+++ +H  APGE Y +G FLVGAYQ
Sbjct: 478 LQRLGEEPTRRAVIQDMTCDSDGRINAYIDRQSIENTLRMHAPAPGEPYLIGFFLVGAYQ 537

Query: 550 EILGDMHNLFGDTDSVNVYQREDGSYYHAGIETHDTIEDMLRYVHLSPEELMTYYRDKVA 609
           EILGDMHNLFGDT SV+V     G Y        D  +D+LRYVH+ P+EL   YR K+ 
Sbjct: 538 EILGDMHNLFGDTHSVDVELDGAGGYTFTHTRRGDGADDLLRYVHIDPDELERSYRKKLI 597

Query: 610 SAKLSAKERTQYIDALRLGLTRSSYL 635
            A +   +R QY   L  GL+  +YL
Sbjct: 598 EADIPMHQRKQYESELIAGLSNYTYL 623


Lambda     K      H
   0.318    0.135    0.391 

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: 1005
Number of extensions: 46
Number of successful extensions: 5
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: 637
Length of database: 625
Length adjustment: 38
Effective length of query: 599
Effective length of database: 587
Effective search space:   351613
Effective search space used:   351613
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 WP_010961291.1 MCA_RS10020 (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.28828.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-247  807.1   0.0   6.2e-247  806.9   0.0    1.0  1  lcl|NCBI__GCF_000008325.1:WP_010961291.1  MCA_RS10020 biosynthetic arginin


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010961291.1  MCA_RS10020 biosynthetic arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  806.9   0.0  6.2e-247  6.2e-247       1     624 []       6     624 ..       6     624 .. 0.99

  Alignments for each domain:
  == domain 1  score: 806.9 bits;  conditional E-value: 6.2e-247
                                 TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqk 69 
                                               w++++++++Y i++W++gyf++  eGev+v+p+  + +  ++++++   v+a+gl+lP+l+rFp+il++
  lcl|NCBI__GCF_000008325.1:WP_010961291.1   6 WTLSDARDTYAIEHWSDGYFNIAPEGEVVVCPQRGSVEGGVSIAAIARGVRAEGLSLPVLMRFPHILHD 74 
                                               788999***************************99999******************************* PP

                                 TIGR01273  70 rikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpEllialalaekpk 138
                                               r++ l++aF +a+  ++Y + y+ vyPiKvnqqr+v+e++++ g   +GLEaGsK+Ell+ lalae  +
  lcl|NCBI__GCF_000008325.1:WP_010961291.1  75 RVRLLTSAFGKARAAYHYGAGYTPVYPIKVNQQRNVIENILRAG--GVGLEAGSKSELLAILALAE--S 139
                                               *******************************************8..89*****************9..8 PP

                                 TIGR01273 139 avivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwas 207
                                                +i+cnGyKDr+yi+lali+ +lgl v+iv+ekl+El+lv+ e++ lg+ P+lG+R+rL+s  +gkw++
  lcl|NCBI__GCF_000008325.1:WP_010961291.1 140 GTIICNGYKDRAYIRLALIGSRLGLRVFIVVEKLSELELVVSESEALGIAPQLGVRIRLSSISAGKWQN 208
                                               88******************************************************************* PP

                                 TIGR01273 208 sgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvki 276
                                               sgGeksKFGL a ++l+ +k+l++++ l +++l+HfH+Gsq+ani+dvk+++rEa+r+y+elr+lG+++
  lcl|NCBI__GCF_000008325.1:WP_010961291.1 209 SGGEKSKFGLHAGEILKFLKRLERAGGLGWVRLMHFHMGSQVANINDVKTALREASRYYAELRRLGAPV 277
                                               ********************************************************************* PP

                                 TIGR01273 277 evvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvpePviisEsGRaitahhavlv 345
                                               ++vdvGGGLg+dY+Gt+s sd+s+nYs++eya+++v a++e c e+g+p+P++i+E+GRa++ahhavlv
  lcl|NCBI__GCF_000008325.1:WP_010961291.1 278 DHVDVGGGLGIDYEGTHSVSDCSINYSVDEYAHSIVRAFSELCAEQGLPQPDLITEAGRAMSAHHAVLV 346
                                               ********************************************************************* PP

                                 TIGR01273 346 aevleveeeeeeeaeeileeeapeevkeleellkeideesaeelledavqlleeavelfklGkldleer 414
                                               ++v+++e+ +++ ++   +   ++ +k+le+ll+ +d+es+  +++da+ +l+e+ +++ +Gk+ l ++
  lcl|NCBI__GCF_000008325.1:WP_010961291.1 347 TNVVDIEAATYDASPV--SASVAQPLKDLEDLLRRVDSESVLGIYHDAEFDLAETRTMYVQGKIGLDQL 413
                                               **********995544..4469999******************************************** PP

                                 TIGR01273 415 alaeqlalailkkvke.leakekshreildelqeklaekylvnlslFqslPDaWgidqlfPilPlerLd 482
                                               a ae+l+ +++++v++ l+ + ++hr +ldel+e+la+k ++n+s+Fqs+PDaW+idq+fP++Pl+rL 
  lcl|NCBI__GCF_000008325.1:WP_010961291.1 414 AEAERLHATLCREVQQrLDIRLRAHRAVLDELNERLADKLFCNFSVFQSIPDAWAIDQIFPVMPLQRLG 482
                                               ********************************************************************* PP

                                 TIGR01273 483 ekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvHnLFgdte 551
                                               e+p+rrav++D+tCDsDG+i+ +++ q+ie+tl +h+  + e+yl+gfflvGAYqEiLgd+HnLFgdt+
  lcl|NCBI__GCF_000008325.1:WP_010961291.1 483 EEPTRRAVIQDMTCDSDGRINAYIDRQSIENTLRMHAPAPGEPYLIGFFLVGAYQEILGDMHNLFGDTH 551
                                               ********************************************************************* PP

                                 TIGR01273 552 avevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkaeekkqvlelleaglsgy 620
                                               +v+v +++ g+++ +++++gd  +d+l++v++dp+el++++++k  ea++ ++++kq++++l agls+y
  lcl|NCBI__GCF_000008325.1:WP_010961291.1 552 SVDVELDGAGGYTFTHTRRGDGADDLLRYVHIDPDELERSYRKKLIEADIPMHQRKQYESELIAGLSNY 620
                                               ********************************************999********************** PP

                                 TIGR01273 621 pYLs 624
                                               +YL+
  lcl|NCBI__GCF_000008325.1:WP_010961291.1 621 TYLE 624
                                               **96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (625 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 8.26
//
[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