GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00890 in Lutibaculum baratangense AMV1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_023434295.1 N177_RS20200 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:A0A165KER0
         (358 letters)



>NCBI__GCF_000496075.1:WP_023434295.1
          Length = 441

 Score =  256 bits (653), Expect = 1e-72
 Identities = 154/346 (44%), Positives = 209/346 (60%), Gaps = 43/346 (12%)

Query: 9   IIGAVALLVLPLI-LQSFGNAWVR-IADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAV 66
           IIG +AL V  L+    F + +V  ++ + L Y++L  GLNIVVG AGLLDLGYVAFYA+
Sbjct: 103 IIGPLALAVALLLPALPFSDRYVMDLSIMVLTYIMLGWGLNIVVGLAGLLDLGYVAFYAI 162

Query: 67  GAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGD 126
           GAY FAL+A+ H    F               WI +P+A +LAAF+G +LG P L+LRGD
Sbjct: 163 GAYSFALLAT-HFDLGF---------------WICLPLAGILAAFWGVILGFPVLRLRGD 206

Query: 127 YLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKR-----LEVFGF 181
           YLAIVTL FGEIIR+ L N       T GP G+  I    +FGL+  +R      E FG 
Sbjct: 207 YLAIVTLAFGEIIRVVLLNW---YEFTGGPNGILGIPDPTLFGLEFARRGDNTFHEFFGL 263

Query: 182 DINS---VTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKL 238
             +S   +   YY+ L L +++  +  RL+   +GRAW A+REDEIA +++GINT N KL
Sbjct: 264 SYSSMHKIIFLYYIILCLALITNFVTLRLRRLPVGRAWEALREDEIACRSLGINTTNTKL 323

Query: 239 LAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLS 298
            AF +GA FGG +G+ F   QGF+SPESF+ +ES +I+A+VVLGG+G   GV++ A+++ 
Sbjct: 324 TAFAIGAMFGGFAGSFFATRQGFISPESFTFIESALILAIVVLGGLGSQVGVVIAAIVMM 383

Query: 299 ALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344
              E  R              +    R L+  LAM+ IM+ RPRGL
Sbjct: 384 GGFEYFR--------------EFEQYRMLIFGLAMVFIMVWRPRGL 415


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: 414
Number of extensions: 16
Number of successful extensions: 4
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: 358
Length of database: 441
Length adjustment: 31
Effective length of query: 327
Effective length of database: 410
Effective search space:   134070
Effective search space used:   134070
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.

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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