GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Phyllobacterium brassicacearum STM 196

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_106712312.1 CU102_RS17070 ABC transporter ATP-binding protein

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



>NCBI__GCF_003010955.1:WP_106712312.1
          Length = 332

 Score =  403 bits (1035), Expect = e-117
 Identities = 203/332 (61%), Positives = 251/332 (75%)

Query: 17  VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76
           +GS+ L+ + K+FG+  V+  IDL++ DGEFV+FVGPSGCGKSTLLR IAGLED + G +
Sbjct: 1   MGSITLQKVSKSFGTTSVIPEIDLEINDGEFVVFVGPSGCGKSTLLRMIAGLEDLSGGRI 60

Query: 77  QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136
            IDG ++ + APAKRG++MVFQSYALYPH++V  N+   LK  G  K  I++KV  AA +
Sbjct: 61  VIDGKDMSNEAPAKRGLSMVFQSYALYPHMSVYGNIAFPLKMDGQDKTAIDKKVKDAAHI 120

Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196
           L+L  YL RRP +LSGGQRQRVAIGRAIVR+PK FLFDEPLSNLDAALR N RLEI+ LH
Sbjct: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVRQPKAFLFDEPLSNLDAALRGNMRLEISDLH 180

Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256
             LK TMIYVTHDQVEAMT+ADKIVVLNAGRIEQVGSP++LY  P N+FVAGFIGSP+MN
Sbjct: 181 HQLKTTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLDLYRSPRNVFVAGFIGSPRMN 240

Query: 257 FIEAAKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHVEHLGADTIIYIESETVGLLTVR 316
            IE  +     A T+G+RPEH+ +S+  G WKG V   EHLG+DT I+++ + VG +TVR
Sbjct: 241 LIEGQEAAKQSAVTLGVRPEHMRISKTEGTWKGIVGVTEHLGSDTFIHVQVDGVGKITVR 300

Query: 317 LFGEHRYATDDIVHATPVIGSMHRFDADGRVI 348
             G+        V+ TP    +HRFDADG+ I
Sbjct: 301 TDGDFSTEFGQQVYLTPEPARLHRFDADGQAI 332


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: 398
Number of extensions: 11
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: 352
Length of database: 332
Length adjustment: 29
Effective length of query: 323
Effective length of database: 303
Effective search space:    97869
Effective search space used:    97869
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