GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HMIT in Caulobacter crescentus NA1000

Align Probable inositol transporter 2 (characterized)
to candidate CCNA_00857 CCNA_00857 glucose/fructose transport protein

Query= SwissProt::Q9C757
         (580 letters)



>FitnessBrowser__Caulo:CCNA_00857
          Length = 478

 Score =  190 bits (482), Expect = 1e-52
 Identities = 119/356 (33%), Positives = 193/356 (54%), Gaps = 28/356 (7%)

Query: 27  YVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAA 86
           +V  +   A IGG +FGYD+GVI+G    +   F        L ++   + V   ++G A
Sbjct: 24  FVAAIVAVATIGGFMFGYDSGVINGTQEGLESAFN-------LSKLGTGLNVGAILIGCA 76

Query: 87  IGGWANDKL----GRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTA 142
           IG +A  +L    GRR+ ++++  LF++ AI   AA +  + ++ R+  GLGVG AS+  
Sbjct: 77  IGAFAAGRLADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLC 136

Query: 143 PLYISEASPAKIRGALVSTNGFLITGGQFLSYLINLAFTDVTGT-----------WRWML 191
           P+YISE +PA IRG L S    +I  G   +++ N A     G+           WRWM 
Sbjct: 137 PVYISEVTPANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWLGLPAWRWMF 196

Query: 192 GIAGIPALLQFVLMFTLPESPRWLYRKGREEEAKAILRRIYSAEDVEQEIRALKDSVETE 251
            +  IPA + F+ +  +PESPR+L  KG++ +A+AIL R++ A    +++  ++ S+  +
Sbjct: 197 WMQIIPAGVFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQGAKKVEEIRASLSAD 256

Query: 252 ILEEGSSEKINMIKLCKAKTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNR 311
                     + +     K +R  L AG+ L VFQQ VGIN V YY   + Q  GF  + 
Sbjct: 257 -----HKPTFSDLLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTED- 310

Query: 312 TALLLSLVTAGLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGILTGVFYEAAT 367
            +L +++++  L+    +++I  ID+IGRK LL+I   G+ ++LG+LT  F  A T
Sbjct: 311 DSLKINILSGTLSILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATT 366



 Score = 61.2 bits (147), Expect = 9e-14
 Identities = 31/101 (30%), Positives = 54/101 (53%), Gaps = 1/101 (0%)

Query: 453 GWFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSFLS 512
           G  AL+   LY+IFF+   G V W++  E++P + RG    +   A WI+N  ++ SF +
Sbjct: 378 GLTALIAANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFPA 437

Query: 513 LTEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIE 553
           L  A     T+  + + +V++   V   V ET+G  +E ++
Sbjct: 438 LA-AASLPMTYGFYALSAVVSFFLVQKLVHETRGKELEAMQ 477


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: 682
Number of extensions: 31
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 580
Length of database: 478
Length adjustment: 35
Effective length of query: 545
Effective length of database: 443
Effective search space:   241435
Effective search space used:   241435
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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