GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17595 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate 8500829 DvMF_1570 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= uniprot:A0A1N7UBU2
         (233 letters)



>FitnessBrowser__Miya:8500829
          Length = 226

 Score =  123 bits (308), Expect = 3e-33
 Identities = 71/215 (33%), Positives = 115/215 (53%), Gaps = 10/215 (4%)

Query: 12  PMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVLIL 71
           P + +G+ +T+   F A+AL L LG+  + A++  A  +R+    Y    R +P LVL+L
Sbjct: 13  PYILEGSLVTVATVFGAMALGLLLGVPMSVAQVYGALPVRLVVGFYVWFFRGMPILVLLL 72

Query: 72  LIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILSVPVGQLEA 131
           L ++ L          F      +  FTA  + LG    AY ++ FRGAIL++P GQL A
Sbjct: 73  LFYFGL----------FQLIGLNLSAFTASCLVLGMTSAAYQSQIFRGAILALPQGQLRA 122

Query: 132 ATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQNAGKT 191
           A A G+S       ++ PQ +R ++PG  N + +LLK +AL  ++G  +++         
Sbjct: 123 ARALGMSDGTAIRSIVLPQALRLSIPGWSNEYSILLKDSALAFVLGTPEIMARTHFVASR 182

Query: 192 TNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNL 226
           T E L   + AG +Y VIT +  +VL+RLE + ++
Sbjct: 183 TYEHLPLYMTAGALYFVITLIGLKVLRRLEHKLHI 217


Lambda     K      H
   0.327    0.141    0.428 

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: 156
Number of extensions: 8
Number of successful extensions: 1
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: 233
Length of database: 226
Length adjustment: 23
Effective length of query: 210
Effective length of database: 203
Effective search space:    42630
Effective search space used:    42630
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 (21.7 bits)
S2: 46 (22.3 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