GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Phaeobacter inhibens BS107

Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate GFF1917 PGA1_c19490 ABC transporter, inner-membrane protein

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



>FitnessBrowser__Phaeo:GFF1917
          Length = 294

 Score =  279 bits (714), Expect = 5e-80
 Identities = 133/284 (46%), Positives = 189/284 (66%)

Query: 18  RWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQYMRLMDNDRWWVA 77
           +++ +L + P ++IVL+ F G + W+  LSFTNS  +P+  +VGL QY RL    RW V+
Sbjct: 9   KFVARLAITPFVVIVLLIFVGCVGWSVQLSFTNSKLLPNGDFVGLDQYYRLFRTTRWIVS 68

Query: 78  SKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWKWLLN 137
            KN+ LFG  F+S +L+LG  LA+LLDQ+IR E F RT++LYP +LS +VTG AW+W LN
Sbjct: 69  LKNMLLFGVFFVSGALILGFLLAILLDQKIRAEAFFRTIFLYPYSLSFVVTGLAWQWFLN 128

Query: 138 PGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVDQSII 197
           P LGL   +R+ GW  F  DWL DQ   +Y +VIAA+W  SG VMA+ LAGLRGVD  I 
Sbjct: 129 PSLGLQNAVRELGWSSFTFDWLTDQSMAIYTIVIAAIWHGSGLVMALMLAGLRGVDPEIW 188

Query: 198 RAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSSDLPA 257
           RA+++DG     +Y+ IV P L PV F++ ++L+   +K FD+V AMT GGPG ++++PA
Sbjct: 189 RASKIDGIPTWRVYVHIVAPILGPVIFASVVLLSLSVVKGFDIVVAMTNGGPGIATEVPA 248

Query: 258 MFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKRH 301
            F+      R  +G+  A A +ML  V++ L P+LY +   KR+
Sbjct: 249 KFVLDHILERANVGLAMAGATIMLITVISALAPWLYVQHMRKRN 292


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: 313
Number of extensions: 10
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: 294
Length adjustment: 26
Effective length of query: 276
Effective length of database: 268
Effective search space:    73968
Effective search space used:    73968
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