GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Pseudomonas simiae WCS417

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate GFF4322 PS417_22135 sugar ABC transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__WCS417:GFF4322
          Length = 281

 Score =  115 bits (289), Expect = 1e-30
 Identities = 66/208 (31%), Positives = 103/208 (49%), Gaps = 1/208 (0%)

Query: 178 FFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLH 237
           F+N++ +T+PA +I   + A   Y L++  F G  L   L++    +P Q  L+P     
Sbjct: 74  FWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQTVLLPASFTL 133

Query: 238 NAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLP 297
             +G+     G    H  +G+       RNY V +P  +I+ A++DGA  F IF +I+LP
Sbjct: 134 GKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAGFFTIFRQIILP 193

Query: 298 LSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAA 357
           +S P +    I+QF   WND L   VF    +   TV  N +V    T    + +   AA
Sbjct: 194 MSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVN-TSTGAKEYNVDMAAA 252

Query: 358 FVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
            ++    LLV+    ++ VRGL AG+VK
Sbjct: 253 MIAGLPTLLVYVIAGKYFVRGLTAGAVK 280



 Score = 26.2 bits (56), Expect = 0.001
 Identities = 12/33 (36%), Positives = 22/33 (66%)

Query: 14 AVQLSVVGLVVLWLLPTFGLFVSSFRTVEQISS 46
          A+   ++  V+L+L+P   + ++SF+T E ISS
Sbjct: 16 AIYAVLILAVLLYLVPLVVMLLTSFKTPEDISS 48


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: 279
Number of extensions: 13
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 385
Length of database: 281
Length adjustment: 28
Effective length of query: 357
Effective length of database: 253
Effective search space:    90321
Effective search space used:    90321
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