GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Pseudomonas fluorescens GW456-L13

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate PfGW456L13_970 L-cystine uptake protein TcyP

Query= uniprot:A1S570
         (437 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_970
          Length = 463

 Score =  202 bits (515), Expect = 1e-56
 Identities = 140/429 (32%), Positives = 226/429 (52%), Gaps = 27/429 (6%)

Query: 1   MAAAQSSKIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLK 60
           +A  + +   L  K+L+ +  G+  G+ L   +G    V    + G+F ++G  ++  L+
Sbjct: 19  LAQTRHTTWSLAKKVLLALVLGVAFGVTLHTVYGAGNPVLK-ASIGWFDLVGNGYVQLLQ 77

Query: 61  MLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLV------- 113
           M+V+PLVF S++     L   S LG++   T+   LFTTAIA ++ I    L        
Sbjct: 78  MIVIPLVFASILSAVARLHNASSLGKISFLTIGTLLFTTAIAALIGIGLTNLFGLTAEGL 137

Query: 114 ---QPGNASLASESMQYSAKEAP-SLADVLINIVPSNPMKALSEG---NMLQIIIFAVIF 166
                  A L +    Y+ K A  ++  +L++ +P NP   L+     +++ ++IFA   
Sbjct: 138 VAGTQEMARLQTIQTDYAGKVADLNVPQLLLSFIPQNPFADLARAKPTSIISVVIFAAFL 197

Query: 167 GFAISHI----GERGRRVAALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETL 222
           G A   +     E+G++V    D L   +MR+V L+M+L PYGV ALM K+   +    L
Sbjct: 198 GVAALQLLKDDAEKGQKVINAIDTLQAWVMRLVRLVMKLTPYGVLALMTKV---VAGSNL 254

Query: 223 ESVIKYFMLVLVVLLFHG--FVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATL 280
           + +IK    V+V  +  G  FVV+  L+   +G++PL F RK+  V  FAF++ SS AT+
Sbjct: 255 QDIIKLGSFVVVSYIGLGLMFVVHGVLVSA-AGINPLRFFRKIWPVLTFAFTSRSSAATI 313

Query: 281 PVTMEASEHRLGADNKVASFTLPLGATINMDGTA-IMQGVATVFIAQVFGID-LTITDYA 338
           P+++EA   RLG    +ASF    GATI  +G A +   +  V +A   GI+ L     A
Sbjct: 314 PLSIEAQTSRLGIPQSIASFAASFGATIGQNGCAGLYPAMLAVMVAPTVGINPLDPLWIA 373

Query: 339 MVVMTATLASIGTAGVPGVGLVMLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGD 398
            +V   TL+S G AGV G       +VL  +GLPV  +AL++ V+ ++DM RTA+NV+G 
Sbjct: 374 TLVAIVTLSSAGVAGVGGGATFAALIVLPAMGLPVSLVALLISVEPLIDMGRTALNVSGS 433

Query: 399 TVATVVIAK 407
             A  + ++
Sbjct: 434 ITAGAITSQ 442


Lambda     K      H
   0.325    0.139    0.388 

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: 406
Number of extensions: 27
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: 437
Length of database: 463
Length adjustment: 33
Effective length of query: 404
Effective length of database: 430
Effective search space:   173720
Effective search space used:   173720
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: 51 (24.3 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