GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT1 in Paraburkholderia bryophila 376MFSha3.1

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate H281DRAFT_02180 H281DRAFT_02180 amino acid/polyamine/organocation transporter, APC superfamily

Query= CharProtDB::CH_091324
         (622 letters)



>FitnessBrowser__Burk376:H281DRAFT_02180
          Length = 463

 Score =  252 bits (644), Expect = 2e-71
 Identities = 156/428 (36%), Positives = 240/428 (56%), Gaps = 34/428 (7%)

Query: 13  MLRRKVVD----CSREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVI 68
           + R+K V+     S + + L + L   DL  LGVG+ +G G++VL G  A + AGPA+++
Sbjct: 3   LFRKKSVEHMIATSAQNAGLKKALGALDLTFLGVGAIIGTGIFVLTGTGAVQ-AGPALMV 61

Query: 69  SFLIAALASVLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSV 128
           SFLIAA+A   A L Y EF + +P  GS Y YSY T+GEL A+I GW+L+L Y + TS+V
Sbjct: 62  SFLIAAVACGFAALAYAEFASTIPVAGSIYTYSYATLGELAAWIIGWDLMLEYGLATSAV 121

Query: 129 ARAWSATFDELIGKPIGEFSRQHMALN-APGVLAQTPDIF---AVIIIIILTGLLTLGVK 184
           +  WS     L+    G      +AL  APG L     +F   A ++++ +T LL++GV+
Sbjct: 122 SVGWSGYLQSLLS---GFGVSLPVALTAAPGALPGHETLFNLPAFLVMMAITALLSVGVR 178

Query: 185 ESAMVNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFG 244
           ESA +N I   I V+V+  ++  G    +  NW                      FMP G
Sbjct: 179 ESARINNIMVAIKVVVVLLVIAVGVFHVTPANWH--------------------PFMPNG 218

Query: 245 FSGVLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLM 304
           ++GV   AA  F+AF+GFD +++  EEVKNP++ +P+GI+ASL +C + Y  V+A +T +
Sbjct: 219 WNGVFGAAAVMFFAFIGFDSVSSAAEEVKNPKRDLPIGIIASLGVCAVLYVAVAAVVTGI 278

Query: 305 MPYF-CLDIDSPLPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGL 363
           +P     +I  P+  A +  G +     + +G++  + T +L   +   RVI+AM+ DGL
Sbjct: 279 VPSAQFANISHPVSYALQVAGQKWVAGFIDLGAVLGMLTVILVMAYGQTRVIFAMSRDGL 338

Query: 364 LFKFLAKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVL 423
           L   L++++ R  TP   T   G    ++  L  L  L +L++IGTL A+S+V+  VLVL
Sbjct: 339 LPARLSRVHPRFATPFFTTWLVGIFFGLIGALVPLNVLAELINIGTLAAFSMVSIAVLVL 398

Query: 424 R-YQPEQP 430
           R   PE P
Sbjct: 399 RKTHPELP 406



 Score = 64.7 bits (156), Expect = 8e-15
 Identities = 47/140 (33%), Positives = 71/140 (50%), Gaps = 19/140 (13%)

Query: 457 SQTGFLPVAEKFSLKSILSPKNVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREALAE 516
           S+ G LP        S + P+   P  F+  +V I  GL+ AL+    +      E +  
Sbjct: 334 SRDGLLPAR-----LSRVHPRFATPF-FTTWLVGIFFGLIGALVPLNVLA-----ELINI 382

Query: 517 GTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQ 576
           GTL A  +++ +VL        + R+   +   +F+ P VPV+PVL++   ++LM  L  
Sbjct: 383 GTLAAFSMVSIAVL--------VLRKTHPELPRAFRCPGVPVVPVLAVASCVFLMANLQA 434

Query: 577 GTWVRFAVWMLIGFTIYFGY 596
            TWV F VW+LIG  IYFGY
Sbjct: 435 VTWVAFVVWLLIGMVIYFGY 454


Lambda     K      H
   0.324    0.138    0.417 

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: 714
Number of extensions: 37
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 622
Length of database: 463
Length adjustment: 35
Effective length of query: 587
Effective length of database: 428
Effective search space:   251236
Effective search space used:   251236
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: 52 (24.6 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