GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04257 in Ochrobactrum thiophenivorans DSM 7216

Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate WP_094508947.1 CEV31_RS17420 carbohydrate ABC transporter permease

Query= reanno::Smeli:SMc04257
         (305 letters)



>NCBI__GCF_002252445.1:WP_094508947.1
          Length = 278

 Score =  130 bits (326), Expect = 5e-35
 Identities = 87/288 (30%), Positives = 142/288 (49%), Gaps = 14/288 (4%)

Query: 20  KPRRTLSRRNIIVYGTLIVV-ALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPW 78
           +P R LSR  +I   T++++ A+  LLP    +V S K   +I     FA    + F+P 
Sbjct: 3   RPPRFLSRYEVIFANTVVILLAIMTLLPFLWFVVMSFKPADQI-----FAGVDGLFFKPT 57

Query: 79  VKAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTIL 138
           ++ +     GL  +   R  WNS+  +  S ++++ I     YAL+    K       ++
Sbjct: 58  LENYE----GLVTERFMRSMWNSIVTSTVSTVLALVIGIPGAYALSRASLKRDRSLSLLI 113

Query: 139 IVGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFK 198
           +     P      P  +V R +G+  T TGLIIV+  F + ++  L RN+F   P EL +
Sbjct: 114 LASRMAPPVAFAIPYFLVYRNLGILDTKTGLIIVYLTFNLALVVWLMRNFFDATPRELEE 173

Query: 199 AARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNN 258
           AA +DGA  W  + +I+LPMS P  V   +L     WNDF F +  TR       V++ N
Sbjct: 174 AAWIDGASLWGTFIRIVLPMSGPAVVTTGMLCFLYSWNDFFFALTLTRNNAMTAPVEVVN 233

Query: 259 IVNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLF-VRGIAAGAVKG 305
            +N  +G +   +    T++  + P+ ++ +  R + V G+ AGAVKG
Sbjct: 234 FMN-YEGWEWGKIAAGGTLI--MAPVLIFSLLMRKYLVAGMTAGAVKG 278


Lambda     K      H
   0.329    0.145    0.450 

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: 232
Number of extensions: 10
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: 305
Length of database: 278
Length adjustment: 26
Effective length of query: 279
Effective length of database: 252
Effective search space:    70308
Effective search space used:    70308
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 (21.8 bits)
S2: 48 (23.1 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