GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Methanococcus aeolicus Nankai-3

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011972867.1 MAEO_RS00720 ATP-binding cassette domain-containing protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_000017185.1:WP_011972867.1
          Length = 281

 Score =  107 bits (267), Expect = 3e-28
 Identities = 77/241 (31%), Positives = 127/241 (52%), Gaps = 22/241 (9%)

Query: 5   LLKIRDVSKRF-GGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63
           +++ +D+  ++  G  AL+   I++E+G +  L+GPNGAGK+T F    G+ +P +G   
Sbjct: 3   IIEAKDIVYKYPDGTLALDRANISVEKGDMVALLGPNGAGKSTLFLHFNGILKPKSGKIL 62

Query: 64  LDGKP--YSPSAPHEVAKAGIARTFQNI--RLFGEMTVLENVMVGCHVRTKQNVFGAVFR 119
           L G P  Y   +  EV K  +   FQN   +LF   TV ++V            FG +  
Sbjct: 63  LKGAPIKYDAKSLMEVRKT-VGIVFQNSDDQLFAP-TVKQDV-----------AFGPL-- 107

Query: 120 HKAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDE 179
           +   +EEE  + ++ ++ L  VG+  F  +   HLS G ++R+ IA  LA  P+++ LDE
Sbjct: 108 NLGLKEEE--VEKRVKEALKEVGMEGFENKPPHHLSGGQKKRVAIAGILAMHPEIMVLDE 165

Query: 180 PAAGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPAD 239
           P AG++      + +LL K+  EG TI++  HDV L+    N+I V+   K +  G   +
Sbjct: 166 PTAGLDPMGASKIMKLLYKLNKEGITIIISTHDVDLVPIYANKIFVMGKTKIVKSGTVEE 225

Query: 240 V 240
           V
Sbjct: 226 V 226


Lambda     K      H
   0.320    0.138    0.394 

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: 151
Number of extensions: 6
Number of successful extensions: 2
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: 255
Length of database: 281
Length adjustment: 25
Effective length of query: 230
Effective length of database: 256
Effective search space:    58880
Effective search space used:    58880
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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