GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcaP in Pedobacter sp. GW460-11-11-14-LB5

Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate CA265_RS17395 CA265_RS17395 amino acid transporter

Query= TCDB::S6EX81
         (469 letters)



>FitnessBrowser__Pedo557:CA265_RS17395
          Length = 483

 Score =  301 bits (772), Expect = 2e-86
 Identities = 170/456 (37%), Positives = 264/456 (57%), Gaps = 17/456 (3%)

Query: 27  DFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYAEMSTVMPFAG 86
           + + +GVG  +   +F++ G  AA  +GP V  S+++AAL  GF AL YAE ++++P AG
Sbjct: 28  NLILIGVGLTLGAGLFSITGLAAANHSGPAVTLSFVIAALGCGFAALCYAEFASMIPVAG 87

Query: 87  SAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLGFHLPKVLA-NP 145
           SAY++     GE F WI GW L+ EY +  A V   +S  L + LA L  +LP  L  +P
Sbjct: 88  SAYTYSYATMGELFAWIIGWDLVLEYSVGCATVAISWSQYLTKFLASLHIYLPPQLTLSP 147

Query: 146 FGT----DG----GVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAVIAFIIVG 197
           F T    DG    G+++I + LV++L   I+ RG   +  ++ I+V LKV  V+ FI +G
Sbjct: 148 FETAKLADGSTVNGIINIPAALVVVLMTAILIRGTKGSAIVNGIIVFLKVGVVLVFIALG 207

Query: 198 ITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAKNPQKTMP 257
              I PANYHP+IP +    G  G+SG+  G  ++F  +IGFD++AA++ E KNP + +P
Sbjct: 208 WQYIDPANYHPYIPENTGTFGQFGWSGVLRGAGLVFFVFIGFDAVAASAQETKNPARDLP 267

Query: 258 RGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVVTAIALAG 317
            GIIGSLL+  VLF     V+ G+  Y  +A + APV  A++++ Y+ LS+ +    L G
Sbjct: 268 IGIIGSLLVCTVLFGLFGHVMTGLANYKEFANSGAPVAIAIEKTPYAWLSQAIILAILIG 327

Query: 318 MFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVAIVIGAFFPFA 376
               +L  ++A SR+ Y+  +DGLLPK    ++A+   P      L +   +  AF P  
Sbjct: 328 YTSVILIDLMAQSRMFYSISKDGLLPKMFSDVHAKFKTPYKSNIILCVFIGLFAAFVPMN 387

Query: 377 FLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEA--TYKMPFYPVLPALGFIGSLFVFW 434
            + ++ S GTL+AF+ V +GI  LR    K  PEA   +K+PF P++P LG +  + +  
Sbjct: 388 VVGEMTSIGTLLAFLMVCVGILILR----KTNPEAKRPFKVPFVPLIPILGILTCIAMMV 443

Query: 435 GLDVQAKLYSGIWFLIGILIYFAYGNRRSR-KSEEK 469
            L  +  L   +W +IG+ IYF YG + S+ K++E+
Sbjct: 444 FLPWETWLRLAVWLIIGLAIYFWYGKKNSKLKAQEE 479


Lambda     K      H
   0.328    0.143    0.433 

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: 624
Number of extensions: 32
Number of successful extensions: 4
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: 469
Length of database: 483
Length adjustment: 33
Effective length of query: 436
Effective length of database: 450
Effective search space:   196200
Effective search space used:   196200
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: 51 (24.3 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