GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Sinorhizobium meliloti 1021

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate SMc03118 SMc03118 ABC transporter permease

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__Smeli:SMc03118
          Length = 295

 Score =  127 bits (318), Expect = 4e-34
 Identities = 88/290 (30%), Positives = 155/290 (53%), Gaps = 21/290 (7%)

Query: 3   LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWA-NTSGINLWL 61
           L QL+  G+  GS  AL ++GL + +G+LR+ NFAHG    L A++ W   +  GI  W 
Sbjct: 13  LGQLLI-GLINGSFYALLSLGLAIIFGLLRVINFAHGAQYMLGAFMAWLLLSYLGIGYWP 71

Query: 62  SMAL-----GCVGTIIAMFIGEWLLWKPMRARRATATTL--IIISIGLALFLRNGILLIW 114
           ++ L     G +G +I          + M  R  T   L  ++ + GLAL +      ++
Sbjct: 72  ALILAPLLVGLIGAVIE---------RTMLRRLYTLDPLYGLLFTFGLALTIEGTFRYLY 122

Query: 115 GGNNQNYRVP-IVPAQDFMGIKF-EYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVAD 172
           G + Q Y  P ++     +G  F   YR  VI  ++   +   L++++TK+G  +RA  +
Sbjct: 123 GASGQPYATPALLMGGANLGFMFLPIYRGWVIVFSLVICLGTWLMIEKTKLGSYLRAATE 182

Query: 173 NVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGG 232
           N  L +  GINV +++  T+ + A L A+ G +   +  + P MG  +I+ +FA V++GG
Sbjct: 183 NPVLVQSFGINVPFLLTLTYGLGAALAAIAGVLAAPIYQVSPLMGSNIIIVVFAVVVVGG 242

Query: 233 IGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLF 282
           +G+  GAI  G ++G+A+ ++  ++  +  + V  ++M I+L +RP GLF
Sbjct: 243 MGSIMGAIVTGYLLGIAEGLTKVFYPEASNI-VIFVIMAIVLLLRPAGLF 291


Lambda     K      H
   0.329    0.143    0.450 

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: 245
Number of extensions: 14
Number of successful extensions: 3
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: 286
Length of database: 295
Length adjustment: 26
Effective length of query: 260
Effective length of database: 269
Effective search space:    69940
Effective search space used:    69940
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 (21.8 bits)
S2: 48 (23.1 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