GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Klebsiella michiganensis M5al

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate BWI76_RS01820 BWI76_RS01820 maltose transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__Koxy:BWI76_RS01820
          Length = 296

 Score = 89.4 bits (220), Expect = 1e-22
 Identities = 66/213 (30%), Positives = 105/213 (49%), Gaps = 9/213 (4%)

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

Query: 239 AIGIGKGYLG------TWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFT 292
            +G    ++G         A+ G G+ L ++ ++ Y   +   + E A +DGAT +Q F 
Sbjct: 146 RLGQYVPFVGLNTHGGVIFAYMG-GIALHVWTIKGYFETIDGSLEEAAALDGATPWQAFR 204

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

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


Lambda     K      H
   0.323    0.138    0.419 

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: 266
Number of extensions: 13
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: 385
Length of database: 296
Length adjustment: 28
Effective length of query: 357
Effective length of database: 268
Effective search space:    95676
Effective search space used:    95676
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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