GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcaP in Erythrobacter marinus HWDM-33

Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_047094595.1 AAV99_RS13360 amino acid permease

Query= TCDB::S6EX81
         (469 letters)



>NCBI__GCF_001013305.1:WP_047094595.1
          Length = 529

 Score =  229 bits (585), Expect = 1e-64
 Identities = 150/484 (30%), Positives = 245/484 (50%), Gaps = 41/484 (8%)

Query: 17  KHYNQVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYA 76
           K  ++ L     +  G+G II T IF L     AQ AGPG++ ++++A  V    AL YA
Sbjct: 19  KSLHRTLGAFQLMLFGIGCIIGTGIFVLTA-AGAQKAGPGLMLAFVIAGTVCIVAALCYA 77

Query: 77  EMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLA--PL 134
           E+++++P AGSAY++     GE   W  GWAL+ EY IA + V  G+S      +     
Sbjct: 78  EIASMIPVAGSAYTYSYATVGEFIAWTVGWALVLEYAIAASAVSVGWSGYFAGTILGDTF 137

Query: 135 GFHLP-KVLANPF---GTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAV 190
           G  LP  + A P    G  GG +++ ++++ LL   ++  G S++ +++ +LV++KV A+
Sbjct: 138 GISLPVSLTAGPLALGGAPGGFINLPAMVIALLVTWLLMIGTSESAKVNAVLVLIKVTAL 197

Query: 191 IAFIIVGIT--VIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAE 248
            AFI + +T      A ++PF+P      G+G   G     + IF AY+GFD+++  + E
Sbjct: 198 TAFIALTLTSSEFDVARFNPFLPA-GVFGGWGTGVGAVGAAATIFFAYVGFDAVSTAAEE 256

Query: 249 AKNPQKTMPRGIIGSLLIAVV---LFAAVTLVLVGMHPYSAYAGNAAPVG---------- 295
            KNPQ+ +P G++GSLL   V   L AA  +  +G  P     G   P G          
Sbjct: 257 TKNPQRNVPIGLVGSLLFCTVFYILVAAGAIGTIGGQPIMGPGGIPFPAGSEELARQCAL 316

Query: 296 ---------------WALQQSGYSVLSEVVTAIALAGMFIALLGMVLAGSRLLYAFGRDG 340
                            L++ G+  +  V+   A+  +   +L ++ A +R+ +   RDG
Sbjct: 317 PQFSDALVCSNEALAHVLREIGFGAIGNVLGYAAILALPSVILVLLFAQTRIFFVMSRDG 376

Query: 341 LLPKGLGKMNARNLPANGVWTLAIVAIVIG-AFFPFAFLAQLISAGTLIAFMFVTLGIYS 399
           LLP+GL K++ +      V  +  V + IG AFFP   LA + +AGTL AF  V + +  
Sbjct: 377 LLPEGLSKVHPKWKTPYVVTAITGVIVAIGAAFFPVGQLADIANAGTLYAFAMVAVAVMV 436

Query: 400 LRRRQGKDLPEATYKMPFYPVLPALGFIGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYG 459
           LRR         ++++P   ++  +  +G +F+F  L ++A L   +W LIG +IYF Y 
Sbjct: 437 LRRTD--PTRTRSFRVPALMIIGPVTVLGCVFLFLNLPLEAMLVLPVWTLIGCVIYFGYS 494

Query: 460 NRRS 463
              S
Sbjct: 495 RGSS 498


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: 700
Number of extensions: 39
Number of successful extensions: 5
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: 529
Length adjustment: 34
Effective length of query: 435
Effective length of database: 495
Effective search space:   215325
Effective search space used:   215325
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: 52 (24.6 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