GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Croceitalea dokdonensis DOKDO 023

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate WP_054558634.1 I595_RS06915 dicarboxylate/amino acid:cation symporter

Query= uniprot:A1S570
         (437 letters)



>NCBI__GCF_001306415.1:WP_054558634.1
          Length = 437

 Score =  294 bits (753), Expect = 3e-84
 Identities = 170/427 (39%), Positives = 257/427 (60%), Gaps = 30/427 (7%)

Query: 8   KIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLV 67
           K+ L  +ILIGM AG+L G  +     G ++V D+I       +GTIF+  LK++ +PL+
Sbjct: 3   KLELHWQILIGMIAGVLFGFAMNQLDWGEQFVADWIRP-----LGTIFVKLLKLIAIPLI 57

Query: 68  FISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPG----------- 116
             SLV G   L + SK   +G +T+A Y+ TT +A+ + +    ++QPG           
Sbjct: 58  LASLVKGVSDLKDISKFRSIGLRTMAIYMGTTLVAITIGLVLVNVIQPGVAIPADTISKL 117

Query: 117 ------NASLASESMQYSAKEAPSLADVLINIVPSNPMKALSEGN-MLQIIIFAVIFGFA 169
                 ++ + S+  + S ++       L  +VP N + A+S+ + MLQ+I F +  G +
Sbjct: 118 VDTYSGDSGVTSKLAEASMQKERGPLQFLEEMVPDNAVYAMSDNSLMLQVIFFTIFLGIS 177

Query: 170 ISHIGE-RGRRVAALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLG-METLESVIK 227
           +  +G+ R + +   F+ LN+V++++V LIM  AP  VFAL+  + ++    + L +++K
Sbjct: 178 MLLVGQKRAKPLKKFFNSLNDVVLKMVDLIMLTAPVAVFALLASVVVSSSDPDLLLALLK 237

Query: 228 YFMLVLVVLLFHGFVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEAS 287
           Y  +VL+ LL    + Y  ++  F+G  PL F+ K+   QL AFST+SS ATLPVTME  
Sbjct: 238 YAGVVLLGLLLM-VLFYCVIISFFTGYHPLKFLIKISPAQLLAFSTSSSAATLPVTMERV 296

Query: 288 EHRLGADNKVASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLA 347
           E  +G D +V+SF LP+GAT+NMDGT++ QGVA VFI+Q    DLT  D   +V TA LA
Sbjct: 297 EEHIGVDAEVSSFVLPVGATVNMDGTSLYQGVAAVFISQALAFDLTFPDQLTIVFTALLA 356

Query: 348 SIGTAGVPGVGLVMLAMVLNQVGLPVE----GIALILGVDRMLDMVRTAVNVTGDTVATV 403
           SIG+A VPG G+VML +VL  +G P +    G+ALI  VDR LDM RT VNVTGD++  +
Sbjct: 357 SIGSAAVPGAGMVMLVIVLEAIGFPADKLAIGLALIFAVDRPLDMCRTVVNVTGDSMVAI 416

Query: 404 VIAKSEG 410
           ++AKS G
Sbjct: 417 LVAKSVG 423


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: 378
Number of extensions: 11
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: 437
Length adjustment: 32
Effective length of query: 405
Effective length of database: 405
Effective search space:   164025
Effective search space used:   164025
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 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