GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Pseudovibrio axinellae Ad2

Align Fructose import permease protein FrcC (characterized)
to candidate WP_068000560.1 PsAD2_RS00560 ABC transporter permease

Query= SwissProt::Q9F9B1
         (360 letters)



>NCBI__GCF_001623255.1:WP_068000560.1
          Length = 332

 Score =  194 bits (492), Expect = 4e-54
 Identities = 123/310 (39%), Positives = 175/310 (56%), Gaps = 20/310 (6%)

Query: 56  VLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSV 115
           +L+LI F  I    F +A  +T IL QV I  I+    T VIL  GIDLSVG++M  +SV
Sbjct: 31  LLALILFFSIFTEHFLTANNITNILTQVTINLILAVGMTFVILIGGIDLSVGSVMAFASV 90

Query: 116 IMGQFTFRYGFPP----ALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLAS 171
           I G+     G  P     L+VI    VG +CG INGT+ AR  LP FI+TLGM  I   +
Sbjct: 91  IAGKAITLAGLGPFEAIVLAVIAATAVGVVCGAINGTITARWSLPSFIITLGMLNIARGA 150

Query: 172 NFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVL----LVCLLWYVLNR 227
               S  +TI +  ++               G+A+F YGV V+ +    LV + W++LN 
Sbjct: 151 ALQASNAQTIYSFPLAFED-----------FGSAMF-YGVPVVFMVALALVFIAWFILNF 198

Query: 228 TAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQF 287
           T +GR +Y +G++ EA +LAG +V R  I+ +T+ GL   +A    + R+   SP AG  
Sbjct: 199 TVFGRLLYGIGNNEEAVRLAGHSVYRYKIAAFTICGLTAGIAAVVYMARLNISSPIAGIG 258

Query: 288 ANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIII 347
             + +I AV+IGG SL GGRGS++G L GA I+GV + GL L+G       ++ G++III
Sbjct: 259 FELNAIAAVIIGGTSLNGGRGSVIGTLIGAFIIGVLANGLILIGLSDFMRQMITGVVIII 318

Query: 348 AVAIDQWIRK 357
           AV +D +  K
Sbjct: 319 AVILDYYRAK 328


Lambda     K      H
   0.327    0.141    0.420 

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: 371
Number of extensions: 20
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: 360
Length of database: 332
Length adjustment: 29
Effective length of query: 331
Effective length of database: 303
Effective search space:   100293
Effective search space used:   100293
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: 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