GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Dinoroseobacter shibae DFL-12

Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate 3608246 Dshi_1650 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= BRENDA::P68183
         (296 letters)



>FitnessBrowser__Dino:3608246
          Length = 385

 Score = 90.5 bits (223), Expect = 5e-23
 Identities = 68/213 (31%), Positives = 107/213 (50%), Gaps = 9/213 (4%)

Query: 86  WNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVALYALFD 145
           +N++ V   + I  + ++   AYA A M FPG+A L+  ++   + P  L+L+ L  L +
Sbjct: 179 FNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHN 238

Query: 146 RLGEYIPFIGLNTHGGVIFAYLG-GIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFR 204
            +G     IG   + G   A+ G G+ L ++ ++ Y   +   + E A +DGAT +Q F 
Sbjct: 239 AIG-----IGKG-YLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFT 292

Query: 205 LVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQ--QYLNPQNYLWGD 262
            ++LPLS P LA   I  F+    ++ VA + L D    T  +  Q  + L  +   W  
Sbjct: 293 KIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEI 352

Query: 263 FAAAAVMSALPITIVFLLAQRWLVNGLTAGGVK 295
            A AA +S     +VF   QR+LV GL AG VK
Sbjct: 353 LATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385


Lambda     K      H
   0.328    0.141    0.435 

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: 315
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 296
Length of database: 385
Length adjustment: 28
Effective length of query: 268
Effective length of database: 357
Effective search space:    95676
Effective search space used:    95676
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: 49 (23.5 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