GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Marinobacter adhaerens HP15

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  298 bits (762), Expect = 2e-85
 Identities = 150/292 (51%), Positives = 205/292 (70%), Gaps = 30/292 (10%)

Query: 17  VGSLQLKTIRKAFG--SHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSG 74
           +  L+L++IRK +   + E LKGID+D+  GEF+I VGPSGCGKSTL+ TIAGLE  T G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 75  SVQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAA 134
           S+ +DG ++  + P  R IAMVFQSYALYP ++V++N+  GLK  G+PK EI+++V + A
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 135 GMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIAR 194
            +L + P + ++PA LSGGQ+QRVA+GRA+ R P+++LFDEPLSNLDA LRV  R EI +
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 195 LHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQ 254
           LH+ LK T++YVTHDQ+EAMTLAD+I VL  G ++Q+G+P E+Y+RP NLFVAGF+GSP 
Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240

Query: 255 MNFI-----------EAAKLGD-----------------GEAKTIGIRPEHI 278
           M+F+           +A   G+                 G+   +GIRPEHI
Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHI 292


Lambda     K      H
   0.320    0.137    0.393 

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: 366
Number of extensions: 11
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 352
Length of database: 372
Length adjustment: 29
Effective length of query: 323
Effective length of database: 343
Effective search space:   110789
Effective search space used:   110789
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: 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