GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Microvirga lotononidis WSM3557

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_009493201.1 MICLODRAFT_RS27670 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::Phaeo:GFF2754
         (331 letters)



>NCBI__GCF_000262405.1:WP_009493201.1
          Length = 363

 Score =  329 bits (843), Expect = 7e-95
 Identities = 183/358 (51%), Positives = 225/358 (62%), Gaps = 27/358 (7%)

Query: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60
           M  + L  V KSFG  E+L+DI+L+V+DGEFVVFVGPSGCGKSTLLR+I+GLE  + GEI
Sbjct: 1   MADVSLHGVAKSFGATEILRDIDLSVDDGEFVVFVGPSGCGKSTLLRIIAGLETVSGGEI 60

Query: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120
            I  + V   PPA R IAMVFQSYALYPH++V +NMA  LK  +  K E+  RV +A+ +
Sbjct: 61  RIDSRRVNELPPADRKIAMVFQSYALYPHMNVYKNMAFGLKFAKTDKAEVDRRVRQAAEI 120

Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180
           L L   LDR+P ELSGGQRQRVAIGRA+VR P +FLFDEPLSNLDAALR+NTRLEIA+LH
Sbjct: 121 LKLTPLLDRKPRELSGGQRQRVAIGRAIVRNPSVFLFDEPLSNLDAALRVNTRLEIAKLH 180

Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240
           R L A+MIYVTHDQ+EAMTLA KIVV+  GRIEQVG P+ELY  P N FVA FIG+P MN
Sbjct: 181 RDLGATMIYVTHDQVEAMTLASKIVVMNHGRIEQVGAPLELYRFPRNLFVAGFIGSPRMN 240

Query: 241 FVPAQ-------------------------RLGGNPGQFIGIRPEYARI--SPVGPLAGE 273
           F+  Q                          L       IGIRPE+  +  +    L G 
Sbjct: 241 FIKGQVLRVEGSSATIGFAGTEALVDVRTGSLSAGDSVTIGIRPEHMEVGGADATSLRGT 300

Query: 274 VIHVEKLGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQRI 331
           +  VE+LG  + + + +        R  G+ D   G +            FD +G  +
Sbjct: 301 IDAVEQLGESSYVYMRLASGDDVIVRAPGETDAAPGGSYTAHVPRRALHVFDASGMSV 358


Lambda     K      H
   0.320    0.137    0.391 

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: 360
Number of extensions: 7
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: 331
Length of database: 363
Length adjustment: 29
Effective length of query: 302
Effective length of database: 334
Effective search space:   100868
Effective search space used:   100868
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 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