GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Marivita geojedonensis DPG-138

Align ABC transporter permease (characterized, see rationale)
to candidate WP_085637763.1 MGEO_RS11965 sugar ABC transporter permease

Query= uniprot:A0A165KPZ4
         (293 letters)



>NCBI__GCF_002115805.1:WP_085637763.1
          Length = 290

 Score =  367 bits (942), Expect = e-106
 Identities = 174/279 (62%), Positives = 220/279 (78%)

Query: 11  PKLVVAPAFVLGFAFIYGLMVWNGVLSLTVSRMLPNYEWAGLAQYERLWEMDRWWVALKN 70
           PKLV+AP+F+    F+YG + W   +S T SR+LP Y+  GL QYERL+   RW  AL N
Sbjct: 10  PKLVLAPSFIAVLIFVYGFIAWTAWVSFTRSRLLPRYDIEGLIQYERLFASPRWDTALNN 69

Query: 71  LGIFGVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWLLNPGL 130
           L +FG+ ++  ++++G++LA+LLDQ IR EGA+RTIYLYPMALS +VTGTAWKW+LNPGL
Sbjct: 70  LFVFGILFILIAMVLGLILAILLDQNIRTEGAIRTIYLYPMALSMIVTGTAWKWILNPGL 129

Query: 131 GIEKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSIIKAA 190
           G+E MVR WGF +F F WLV+ +MAIY VVIA IWQS+GF MALFLAGLR +D  IIKAA
Sbjct: 130 GVEAMVRGWGFESFTFDWLVNPDMAIYTVVIAAIWQSSGFVMALFLAGLRSVDGEIIKAA 189

Query: 191 QVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFATDVPATFM 250
           QVDG    RIY  I++P++ P+F S  +VLSHLAIKSFDLV+ALT GGPG+ATD+PAT+M
Sbjct: 190 QVDGIPTWRIYTAIIIPSMAPIFLSAFIVLSHLAIKSFDLVIALTGGGPGYATDLPATYM 249

Query: 251 YTMSFSRGQIGLGAASATMMLATVAALVIPYLYSELRTK 289
           Y M+FSRG IG  A+SA +M+  V A+V+PYLYSELR+K
Sbjct: 250 YAMAFSRGDIGQAASSAMIMMMVVFAIVVPYLYSELRSK 288


Lambda     K      H
   0.327    0.141    0.451 

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: 368
Number of extensions: 13
Number of successful extensions: 1
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: 293
Length of database: 290
Length adjustment: 26
Effective length of query: 267
Effective length of database: 264
Effective search space:    70488
Effective search space used:    70488
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: 48 (23.1 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