GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Shewanella amazonensis SB2B

Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate 6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= BRENDA::Q5XPV2
         (457 letters)



>FitnessBrowser__SB2B:6938908
          Length = 404

 Score =  117 bits (293), Expect = 7e-31
 Identities = 100/339 (29%), Positives = 160/339 (47%), Gaps = 43/339 (12%)

Query: 124 RLFFVDGGALAVENALKAALDWKAQKLGLAEPDTDRLQVLHLERSFHGRSGYTMSLTNTE 183
           R++F + GA A E ALK A  +  +K G       +++V+  +++FHGR+ +T+S+    
Sbjct: 100 RVYFANSGAEANEAALKLARRYAIEKFG-----EHKVEVIAFDKAFHGRTFFTVSVGGQA 154

Query: 184 PSKTARFPKFGWPRISSPALQHPPAEHTGANQEAERRALEAAREAFAAADGMIACFIAEP 243
                  PK         A+ H P     A        LEAA      +D   A  + EP
Sbjct: 155 AYSDGFGPK-------PAAITHLPFNDIAA--------LEAA-----VSDNTCAIML-EP 193

Query: 244 IQGEGGDNHLSAEFLQAMQRLCHENDALFVLDEVQSGCGITGTAWAYQQLGLQPDLVAFG 303
           +QGEGG  +   EFL+A++RL  +++AL + DEVQ+G G TG  +AY    + PD++   
Sbjct: 194 LQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLYAYMGTEIVPDILTTA 253

Query: 304 KKTQVCGVMGGGRIDEVPENVFAVSSRI-----SSTWGGNLADMVRATRLLETIERTQVF 358
           K       +GGG           ++S +      ST+GGN         +++ +   +V 
Sbjct: 254 K------ALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVL 307

Query: 359 DTVVQRGKYFRDGLEDLAARHPSVVTNARGRGLMCAVDLPDT---RTRNEVLRLMYTEHQ 415
           D V  R + FRDGL  +  ++  V +  RG+GL+    L +    R+R + L     E  
Sbjct: 308 DGVKHREQLFRDGLAQINEKY-HVFSEIRGKGLLLGAVLNEQFAGRSR-DFLNASVAE-G 364

Query: 416 VIALPCGGRSLRFRPALTIAEHEIDQALQALASSVTAVA 454
           ++ L  G   +RF P+L I E +I + L     +V  VA
Sbjct: 365 LLTLMAGANVVRFTPSLVIPEADIVEGLARFERAVAKVA 403


Lambda     K      H
   0.320    0.135    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: 402
Number of extensions: 17
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: 457
Length of database: 404
Length adjustment: 32
Effective length of query: 425
Effective length of database: 372
Effective search space:   158100
Effective search space used:   158100
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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