GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Slc7a1 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02180 H281DRAFT_02180 amino
           acid/polyamine/organocation transporter, APC superfamily
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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