GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Jannaschia aquimarina GSW-M26

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_043917695.1 jaqu_RS04205 acyl-CoA dehydrogenase family protein

Query= BRENDA::Q3JP94
         (395 letters)



>NCBI__GCF_000877395.1:WP_043917695.1
          Length = 387

 Score =  188 bits (478), Expect = 2e-52
 Identities = 118/375 (31%), Positives = 190/375 (50%), Gaps = 2/375 (0%)

Query: 18  LADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGL 77
           L +D   +R+  H +AQ ++ P  +E          ++ EMGE+GLLG T+PE+ GG G+
Sbjct: 10  LGEDVEALREMVHRWAQDRVKPMASEIDGSNAFPNDLWSEMGELGLLGITVPEEDGGAGM 69

Query: 78  DYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFG 137
            Y+++ +   E+ R  +         S+L +  I   G   QK +YLP L +G  +G   
Sbjct: 70  GYLAHTVAIEEIARASASVSLSYGAHSNLCVNQIALNGDADQKARYLPDLISGAAVGALA 129

Query: 138 LTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDEIRGF 196
           ++E   GSD   M  RA K    Y L+G+K WITN P A   VV+AK D E G   I  F
Sbjct: 130 MSEAGAGSDVVGMKLRADKRNDRYVLNGTKYWITNGPDASTLVVYAKTDPEAGSRGITAF 189

Query: 197 ILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNSARY 255
           ++EK  KG S      K+G+R S T E++ ++  VP EN+L    +G++   + L+  R 
Sbjct: 190 LVEKAMKGFSTSPHFDKLGMRGSNTAELIFEDVEVPFENVLGEEGRGVQVLMSGLDYERV 249

Query: 256 GIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGR 315
            +A   LG   +C      Y+ +R+QFG+P+ + QL+Q K+ADM T +      V    +
Sbjct: 250 VLAGIGLGIMAACLDEIMPYLAERRQFGKPIGSFQLMQGKIADMYTAMNSARAYVYEAAK 309

Query: 316 MKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEG 375
             D G    +  +     +  +A+  A  A   +GG G  ++  V+R   + +++    G
Sbjct: 310 ACDRGEVTRQDAAACCLYASEQAMVQAHQAVQAMGGAGFMNDTPVSRLFRDAKLMEIGAG 369

Query: 376 THDIHALILGRAQTG 390
           T +I  +++GR   G
Sbjct: 370 TSEIRRMLVGRELMG 384


Lambda     K      H
   0.320    0.138    0.414 

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: 335
Number of extensions: 14
Number of successful extensions: 3
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: 395
Length of database: 387
Length adjustment: 31
Effective length of query: 364
Effective length of database: 356
Effective search space:   129584
Effective search space used:   129584
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: 50 (23.9 bits)

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:

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:

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:

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:

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