GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araWsh in Phyllobacterium brassicacearum STM 196

Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_106713880.1 CU102_RS25515 ABC transporter permease

Query= uniprot:A0KWY6
         (405 letters)



>NCBI__GCF_003010955.1:WP_106713880.1
          Length = 331

 Score =  205 bits (522), Expect = 1e-57
 Identities = 118/312 (37%), Positives = 196/312 (62%), Gaps = 16/312 (5%)

Query: 66  LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDL 125
           +LAL +L+L NL    +F  +         +L   L +   + ++++GM+LVIATGGIDL
Sbjct: 26  ILALVLLILFNLAFTRNFATMQ--------TLNVNLTQVCTIVIVAVGMTLVIATGGIDL 77

Query: 126 SVGAVMAIAGAVCANLLL---VPDISLVTVIAAGLIVGL----LAGCINGGLVSFLGIQP 178
           SVG++MAI+GA+   + L   VP  S+   + A +++ +    L G  NG L++   IQP
Sbjct: 78  SVGSLMAISGALAPMIFLGKIVPIDSVGIAVVAAMVISVGVAGLFGLFNGWLIAKFRIQP 137

Query: 179 IVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLL 238
           IVATL+L +AGRG+AQ++  G + TF+ P F  IG+G+  G+P+ V +++ ++  +  +L
Sbjct: 138 IVATLVLFIAGRGIAQVMTNGNLQTFRVPQFQFIGLGRVFGVPVQVVLMLLLVIAAAWVL 197

Query: 239 RKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNA 298
           ++T  G  I A+G N +A+   GI   ++KL  Y I+GLCA +AG++  A    SDAN  
Sbjct: 198 KRTVFGRQIIAIGGNERAAELSGIAVSTVKLVVYTISGLCAGVAGLVVIAINSSSDANLV 257

Query: 299 GLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKA-I 357
           GL +ELDA+ AV +GG  L+GG+ +++ +++GA+ IQ +  T++ +G+P    L++KA I
Sbjct: 258 GLGMELDAIAAVAVGGTLLSGGKATIVGTLLGAMTIQLVRYTLLANGVPDAAALVVKAGI 317

Query: 358 VILTVLLLQSAK 369
           ++L V + Q  +
Sbjct: 318 IVLAVWIQQQGR 329


Lambda     K      H
   0.323    0.136    0.379 

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: 348
Number of extensions: 24
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: 405
Length of database: 331
Length adjustment: 30
Effective length of query: 375
Effective length of database: 301
Effective search space:   112875
Effective search space used:   112875
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 24 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