GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Flavobacterium beibuense F44-8

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_035136158.1 Q763_RS16555 ABC transporter ATP-binding protein

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



>NCBI__GCF_000769915.1:WP_035136158.1
          Length = 234

 Score =  125 bits (315), Expect = 8e-34
 Identities = 78/219 (35%), Positives = 122/219 (55%), Gaps = 12/219 (5%)

Query: 20  LQLKTIRKAFGSHEV----LKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGS 75
           ++++ + K F + EV    L  I ++VK GEFV  +G SGCGKSTLL  +  L+ A+ GS
Sbjct: 2   IKIENLSKVFRTEEVETKALNDISIEVKKGEFVTIMGASGCGKSTLLNIVGLLDSASGGS 61

Query: 76  VQIDGVEVGHVAPA------KRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEK 129
            ++   E+  ++ +      K  I  VFQ++ L   L+V DN+ L L    VP  E +++
Sbjct: 62  YKLLDREINGLSESEKAKVRKENIGFVFQNFNLIDELSVYDNIELPLIYNNVPSGERKKR 121

Query: 130 VAKAAGMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTR 189
           V + A  L +   L   P +LSGGQ+QR A+ RA+V  PK+ L DEP  NLD+    N  
Sbjct: 122 VEEIAERLGISHRLKHYPQQLSGGQQQRAAVARALVNNPKIILADEPTGNLDSK-NGNEV 180

Query: 190 LEIARLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRI 228
           +E+     +  AT++ VTH + +A + + K + +  G I
Sbjct: 181 MELLTDLHANGATILMVTHSEYDA-SFSQKTIYMKDGMI 218


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: 165
Number of extensions: 9
Number of successful extensions: 2
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: 352
Length of database: 234
Length adjustment: 26
Effective length of query: 326
Effective length of database: 208
Effective search space:    67808
Effective search space used:    67808
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: 47 (22.7 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