GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_043917831.1 jaqu_RS04945 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KER0
         (358 letters)



>NCBI__GCF_000877395.1:WP_043917831.1
          Length = 429

 Score =  105 bits (261), Expect = 3e-27
 Identities = 114/418 (27%), Positives = 176/418 (42%), Gaps = 85/418 (20%)

Query: 13  VALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFA 72
           VALL L        N  + I ++A++  ++ALG+N+  GYAGL ++G + F A+G     
Sbjct: 11  VALLFLGTGFVQSWNVALTILNMAMVSAIMALGVNMQWGYAGLFNVGVMGFVALGGLGAV 70

Query: 73  LMASPHLAD--------------------------------------------NFAAFAA 88
           L+  P + +                                             F AF A
Sbjct: 71  LVGMPPVNEAWAAGGLRVVGGLLIGAATIAAAVMAWDRMRRFRGLAVAALLLIGFFAFRA 130

Query: 89  MFPNGLHT---------------SLWIVI--PVAALLAAFFGAMLGAPTLKLRGDYLAIV 131
           +F  G+                  L I+I  PV  LLAA     +G   L LR DYLAI 
Sbjct: 131 VFDGGVQMVEAVNPASTGYLGGLGLPIIIGWPVGGLLAAGAAWFIGKTALGLRSDYLAIA 190

Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLG-----QID-----SVKVFGLDLGKRLEVFGF 181
           TLG  EI+   L N D          GL      ++D       + F  +LG    V   
Sbjct: 191 TLGIAEIVIAVLKNEDWLARGVKNVIGLPRPVPYEVDLQNSAGFREFAAELGTD-PVTAS 249

Query: 182 DINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAF 241
            I     Y  LF V++ + + +      S  GR   AIR++E+AA+AMG +     L  F
Sbjct: 250 TIAVKLAYLGLFGVVLGLLLWLAQAALASPWGRMMRAIRDNEVAAEAMGKDVTARHLQIF 309

Query: 242 GMGASFGGVSGAMFGAFQGFVSPESFS-LMESVMIVAMVVLGGIGHIPGVILGAVLLSAL 300
            +G++  G++GAM     G ++P ++  L  + +I  MV++GG G+  G +LG  L+  L
Sbjct: 310 ILGSAVCGLAGAMMTTLDGQLTPGTYQPLRYTFLIWVMVIVGGSGNNWGAVLGGFLIWWL 369

Query: 301 -PEVLRYVAGPLQAMTDGRLD-----------SAILRQLLIALAMIIIMLLRPRGLWP 346
             +V    A  +  +T G  D           +A +R L + L +++++   PRGL P
Sbjct: 370 WVQVEPLGALLMDTITAGMADGTWLKGHLQDAAAHMRLLTMGLVLLLVLRFSPRGLIP 427


Lambda     K      H
   0.328    0.144    0.430 

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: 427
Number of extensions: 23
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 358
Length of database: 429
Length adjustment: 31
Effective length of query: 327
Effective length of database: 398
Effective search space:   130146
Effective search space used:   130146
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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