GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcF in Phaeobacter inhibens BS107

Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component

Query= TCDB::Q8RJU9
         (308 letters)



>FitnessBrowser__Phaeo:GFF1647
          Length = 316

 Score =  139 bits (350), Expect = 9e-38
 Identities = 94/294 (31%), Positives = 151/294 (51%), Gaps = 19/294 (6%)

Query: 12  FLAVPLGLYALLVVWPFIQSIYYSFTDWTGLSPDFKT--VGFDNYERMLDDDIFWKSLQH 69
           +L+  + L   +++ P I  I YSF     L+P F T  VGF+NYE++  D  FW +L++
Sbjct: 36  YLSPMILLIGSVMLIPLIVGISYSFQSIELLNP-FATGWVGFENYEKLWSDRKFWIALEN 94

Query: 70  SLLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIAIV 129
           +  +          L L  A ++N            T   G   ++ + F P  +   + 
Sbjct: 95  TFFWTFWSIFFQFFLGLGLAMLLN------------TQFFGKKLFQALVFLPWAVPTFLS 142

Query: 130 ALLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLFSA 189
           AL +A+ +NP  G I   L  +G+       LGDPDLA+W  +   +W  V FF +   A
Sbjct: 143 ALTWAWLFNPVIGPIPHWLAALGVLSEPYNILGDPDLAIWGPITANIWFGVPFFAITLLA 202

Query: 190 GMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHIMT 249
            + SIP ++YEAA +DGA    +F +ITLP L   +    + + +  +   +FA +  + 
Sbjct: 203 ALQSIPGELYEAAEIDGATPWQSFTKITLPFLAPMIA---ITVMLRTIWIANFADLIFVM 259

Query: 250 TGPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAAVVMRLGRR 303
           TG GGP  ST ++  Y++  AFR     YA+TI VALLI+ LA+A +++ + +R
Sbjct: 260 TG-GGPANSTQILSTYIFTTAFRKLDFGYASTIAVALLIILLAYAVILLWMRKR 312


Lambda     K      H
   0.330    0.145    0.458 

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: 347
Number of extensions: 29
Number of successful extensions: 4
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: 308
Length of database: 316
Length adjustment: 27
Effective length of query: 281
Effective length of database: 289
Effective search space:    81209
Effective search space used:    81209
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