GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate GFF1858 Psest_1897 ABC-type sugar transport systems, permease components

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895
         (302 letters)



>FitnessBrowser__psRCH2:GFF1858
          Length = 305

 Score =  533 bits (1374), Expect = e-156
 Identities = 260/304 (85%), Positives = 284/304 (93%), Gaps = 3/304 (0%)

Query: 1   MSSVAVFS---KASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSY 57
           MSS+A+ +   KASP DALQRWLPKLVLAPSMLIVLVGFY YI WTF+LSFTNS FMPSY
Sbjct: 1   MSSIALQARPAKASPLDALQRWLPKLVLAPSMLIVLVGFYAYIGWTFLLSFTNSRFMPSY 60

Query: 58  KWVGLQQYMRLMDNDRWWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVY 117
           KWVGLQQY RL DNDRWWVAS+NL +FGG+FI++SL++GV LAVLLDQRIR+EG IRT+Y
Sbjct: 61  KWVGLQQYERLWDNDRWWVASQNLLVFGGLFIAVSLIIGVVLAVLLDQRIRREGLIRTIY 120

Query: 118 LYPMALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQA 177
           LYPMALSMIVTGTAW+WLLNPGLGLDK+LRDWGWEGFR DWLVD DRV+YCLVIAAVWQA
Sbjct: 121 LYPMALSMIVTGTAWQWLLNPGLGLDKLLRDWGWEGFRFDWLVDPDRVIYCLVIAAVWQA 180

Query: 178 SGFVMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKS 237
           SGFVMA+FLAGLR VDQSIIRAAQVDGASLPTIYL+IVLPSLRPVFFSA MILAHIAIKS
Sbjct: 181 SGFVMALFLAGLRSVDQSIIRAAQVDGASLPTIYLRIVLPSLRPVFFSALMILAHIAIKS 240

Query: 238 FDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELR 297
           FDLVAAMTAGGPGYSSDLPAMFMY+ TF+RGQMG+G+ASAMLMLGAV+ I+VPYLYSELR
Sbjct: 241 FDLVAAMTAGGPGYSSDLPAMFMYAHTFTRGQMGLGAASAMLMLGAVMAIIVPYLYSELR 300

Query: 298 GKRH 301
            KRH
Sbjct: 301 NKRH 304


Lambda     K      H
   0.329    0.141    0.448 

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: 476
Number of extensions: 6
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: 302
Length of database: 305
Length adjustment: 27
Effective length of query: 275
Effective length of database: 278
Effective search space:    76450
Effective search space used:    76450
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 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