GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Pseudomonas simiae WCS417

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF3277 PS417_16775 branched-chain amino acid ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__WCS417:GFF3277
          Length = 255

 Score =  166 bits (421), Expect = 3e-46
 Identities = 97/241 (40%), Positives = 145/241 (60%), Gaps = 9/241 (3%)

Query: 4   LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTP-----S 58
           LL V D+   Y   +  + G++ S+  G  V ++G NGAGKST  K I GL+       S
Sbjct: 13  LLSVNDIEVIYDGAILAVAGVSLSVPKGATVALLGANGAGKSTTLKAISGLVRAERAEVS 72

Query: 59  QGEIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLK-- 116
           +G I + G ++ G+   Q VR+GM +V +  +VFG L+V +NL  G F+ +   Q ++  
Sbjct: 73  RGTIEYAGTDLAGIDPSQRVRQGMVHVLEGRHVFGQLSVEDNLRSGGFVRRLSRQEMEHD 132

Query: 117 -DRIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDV 175
            +R+Y  FP+L  +R+ RAG  SGGE+QM+A+GRALM  P L+LLDEPS  L+P++V+++
Sbjct: 133 LERLYAWFPRLKTKRHTRAGLTSGGEQQMVAIGRALMTRPTLVLLDEPSMGLAPMIVQEI 192

Query: 176 FAQIKAINATGK-AIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYL 234
           F  I  +N   + + ++ EQN   AL  A  GYVL+ GR  L GS   LL    + ++YL
Sbjct: 193 FEIIGQLNREQQVSFLIAEQNINVALNYASHGYVLDTGRVALSGSAAELLARGDLHDIYL 252

Query: 235 G 235
           G
Sbjct: 253 G 253


Lambda     K      H
   0.320    0.139    0.393 

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: 144
Number of extensions: 8
Number of successful extensions: 4
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: 240
Length of database: 255
Length adjustment: 24
Effective length of query: 216
Effective length of database: 231
Effective search space:    49896
Effective search space used:    49896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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