GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Phyllobacterium brassicacearum STM 196

Align Fructose import permease protein FruF (characterized)
to candidate WP_106713880.1 CU102_RS25515 ABC transporter permease

Query= SwissProt::Q8G846
         (356 letters)



>NCBI__GCF_003010955.1:WP_106713880.1
          Length = 331

 Score =  166 bits (420), Expect = 8e-46
 Identities = 103/316 (32%), Positives = 172/316 (54%), Gaps = 23/316 (7%)

Query: 24  SIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAG 83
           +I+A +LL++    F  +F  +            L   L +    +++A GMTLVI+T G
Sbjct: 25  TILALVLLILFNLAFTRNFATMQ----------TLNVNLTQVCTIVIVAVGMTLVIATGG 74

Query: 84  IDLSVGSVMAVAGAAAMQTL--------SNGMNVWLSILIALAVGLAIGCVNGALVSFLG 135
           IDLSVGS+MA++GA A            S G+ V  +++I++ V    G  NG L++   
Sbjct: 75  IDLSVGSLMAISGALAPMIFLGKIVPIDSVGIAVVAAMVISVGVAGLFGLFNGWLIAKFR 134

Query: 136 LQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVIIV 195
           +QP + TL++ +AGRG+A+V+T+G N     V      ++   G + G+P   V+ +++V
Sbjct: 135 IQPIVATLVLFIAGRGIAQVMTNG-NLQTFRVP---QFQFIGLGRVFGVPVQVVLMLLLV 190

Query: 196 ILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVM 255
           I    + ++T  G  I A+G N+ A+ ++GI    +  +VY ISG  A +AGL   A   
Sbjct: 191 IAAAWVLKRTVFGRQIIAIGGNERAAELSGIAVSTVKLVVYTISGLCAGVAGLVVIAINS 250

Query: 256 RVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGV-NAEA 314
             D    G  +E+ AI AV +GGT L GGK ++ G+ +GA+ I ++R T++  GV +A A
Sbjct: 251 SSDANLVGLGMELDAIAAVAVGGTLLSGGKATIVGTLLGAMTIQLVRYTLLANGVPDAAA 310

Query: 315 TPAFFAVVVIVICVMQ 330
                 ++V+ + + Q
Sbjct: 311 LVVKAGIIVLAVWIQQ 326


Lambda     K      H
   0.325    0.136    0.384 

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: 316
Number of extensions: 17
Number of successful extensions: 3
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: 356
Length of database: 331
Length adjustment: 29
Effective length of query: 327
Effective length of database: 302
Effective search space:    98754
Effective search space used:    98754
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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