GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HMIT in Pantoea rwandensis LMG 26275

Align Probable inositol transporter 2 (characterized)
to candidate WP_084936573.1 HA51_RS21365 sugar porter family MFS transporter

Query= SwissProt::Q9C757
         (580 letters)



>NCBI__GCF_002095475.1:WP_084936573.1
          Length = 464

 Score =  233 bits (594), Expect = 1e-65
 Identities = 133/341 (39%), Positives = 203/341 (59%), Gaps = 15/341 (4%)

Query: 20  SLTWKNPYVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVA 79
           S T      L + F A + GLLFG D GVI+GAL +I  DF         QE IVS  + 
Sbjct: 8   SRTSNKMMTLFVCFLAALAGLLFGLDIGVIAGALPFIAKDFNVTAHQ---QEWIVSSMMF 64

Query: 80  GAIVGAAIGGWANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMAS 139
           GA VGA   GW + +LGR+ +++    LF++G++  A A +P +L+  RV +GL VG+AS
Sbjct: 65  GAAVGAVGSGWMSSRLGRKKSLMAGAILFVIGSLWSAMATSPDMLIAARVVLGLAVGVAS 124

Query: 140 MTAPLYISEASPAKIRGALVSTNGFLITGGQFLSYLINLAFTDVTGTWRWMLGIAGIPAL 199
            TAPLY+SE +P KIRG+++S    +IT G   +YL + AF+D  G WRWMLG+  IPA+
Sbjct: 125 YTAPLYLSEIAPEKIRGSMISLYQLMITIGILAAYLSDTAFSD-AGAWRWMLGVITIPAI 183

Query: 200 LQFVLMFTLPESPRWLYRKGREEEAKAILRRIY-SAEDVEQEIRALKDSVETEILEEGSS 258
           L  + +F LP SPRWL  KG    A+ +L R+  ++E  ++E+  +++S++         
Sbjct: 184 LLLIGVFFLPNSPRWLAAKGDFRSAQRVLDRLRDTSEQAKRELDEIRESLKI-------- 235

Query: 259 EKINMIKLCKAKT-VRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNRTALLLS 317
            K +  +L ++ +  RR +  GV LQV QQF G+N +MYY+P I ++AGFA+    +  +
Sbjct: 236 -KQSGWQLFQSNSHFRRAVYLGVLLQVMQQFTGMNVIMYYAPKIFEIAGFANTTQQMWGT 294

Query: 318 LVTAGLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGIL 358
           ++   +N   + I+I  +DR GRK  L++    +   +GIL
Sbjct: 295 VIVGLVNVLATFIAIGLVDRWGRKPTLVLGFIVMAAGMGIL 335



 Score = 74.7 bits (182), Expect = 8e-18
 Identities = 34/103 (33%), Positives = 64/103 (62%)

Query: 454 WFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSFLSL 513
           +FA+  L ++I+ F+   G + W++ SEI PL+ R     ++   NWI+N+IV  +FL++
Sbjct: 350 YFAVAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITVSTATNWIANMIVGATFLTM 409

Query: 514 TEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIEKML 556
             ++G + TF ++  ++V  +L  +  +PETK + +E IE+ L
Sbjct: 410 LNSLGNAPTFWVYAGLNVFFILLTVALIPETKNVSLEHIERNL 452


Lambda     K      H
   0.324    0.139    0.425 

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: 679
Number of extensions: 36
Number of successful extensions: 7
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: 580
Length of database: 464
Length adjustment: 35
Effective length of query: 545
Effective length of database: 429
Effective search space:   233805
Effective search space used:   233805
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 (21.5 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