GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Pseudomonas stutzeri RCH2

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate GFF1859 Psest_1898 ABC-type sugar transport system, permease component

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__psRCH2:GFF1859
          Length = 280

 Score =  111 bits (277), Expect = 3e-29
 Identities = 64/208 (30%), Positives = 102/208 (49%), Gaps = 1/208 (0%)

Query: 178 FFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLH 237
           F+N++ + IPA +I   + A   Y L+   F G  L   L++    +P Q+ L+P     
Sbjct: 73  FWNSVKIVIPAVLISTALGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQVILLPASFTL 132

Query: 238 NAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLP 297
             +G+     G  L H  +G+       RN+ V +P  ++  A++DGA  F IF +I+LP
Sbjct: 133 GKLGLANTTTGLVLVHVVYGLAFTTLFFRNFYVSVPDALVRAARLDGAGFFTIFGRILLP 192

Query: 298 LSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAA 357
           +S P +    I+QF   WND L   VF    T   TV  N +V    T    + +   AA
Sbjct: 193 MSVPIIMVCLIWQFTQIWNDFLFGVVFASGDTQPVTVALNNLVN-TSTGAKQYNVDMAAA 251

Query: 358 FVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
            ++    L+V+    ++ +RGL AG+VK
Sbjct: 252 MIAGLPTLVVYVVAGKYFLRGLTAGAVK 279


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: 277
Number of extensions: 15
Number of successful extensions: 2
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: 385
Length of database: 280
Length adjustment: 28
Effective length of query: 357
Effective length of database: 252
Effective search space:    89964
Effective search space used:    89964
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