GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00890 in Marinobacter adhaerens HP15

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF2761 HP15_2705 inner-membrane translocator

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__Marino:GFF2761
          Length = 335

 Score =  166 bits (419), Expect = 1e-45
 Identities = 111/353 (31%), Positives = 177/353 (50%), Gaps = 46/353 (13%)

Query: 1   MKNTKTNWIIGAVALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLG 59
           M++     +I A+ L++LP  L   GN +   +     +     +GLN++VG+AG + LG
Sbjct: 6   MQSRLRGLVILALILVILPAFL---GNPFHYELVTQMAIIAATVVGLNLLVGFAGQISLG 62

Query: 60  YVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAM---L 116
           +  F+ +GAY   +                      T  W  +P   + A   GA+   +
Sbjct: 63  HAGFFGLGAYFTGIATG-------------------TYGWSSVPALVVGAIVVGAIAWIV 103

Query: 117 GAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGK-- 174
           G P L+L+G YL++ TL  G II I LNN      LT GP G+  + + ++FG +L    
Sbjct: 104 GRPILRLKGHYLSMATLAVGFIIAIILNN---ERALTGGPDGM-PVPAFEIFGWELSAFG 159

Query: 175 RLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTR 234
           R  +FG  I     +Y    V+++V+V     L +S IGRA  ++   E+AA  +G+NT 
Sbjct: 160 RYSLFGITIEGFQAWYIFASVVLLVAVWFALNLIESPIGRALRSVHGSEVAASVVGVNTA 219

Query: 235 NMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGA 294
             K L F + A +  + G+++  FQGF++P   S   S++ + MVVLGG+G   GVILGA
Sbjct: 220 KYKSLVFVISAIYASLMGSLYAHFQGFITPAVASFEFSILFITMVVLGGMGSTFGVILGA 279

Query: 295 VLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPS 347
           V+L  LP+VL               D   L  ++  L +++ M+  P+GL P+
Sbjct: 280 VVLKLLPQVL--------------ADFQELEHVMFGLILMLTMIFMPKGLLPT 318


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: 335
Number of extensions: 26
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: 358
Length of database: 335
Length adjustment: 29
Effective length of query: 329
Effective length of database: 306
Effective search space:   100674
Effective search space used:   100674
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: 49 (23.5 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