GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Sinorhizobium meliloti 1021

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate SM_b20611 SM_b20611 C4-dicarboxylate transporter DctA

Query= TCDB::Q01857
         (444 letters)



>FitnessBrowser__Smeli:SM_b20611
          Length = 441

 Score =  713 bits (1840), Expect = 0.0
 Identities = 368/432 (85%), Positives = 400/432 (92%)

Query: 13  KGKKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVAT 72
           +GK P Y HLYVQVL AIAAGILLGHFYP++GT+LKPLGDAFI+LVKMIIAPVIFLTVAT
Sbjct: 10  RGKTPLYRHLYVQVLAAIAAGILLGHFYPDIGTELKPLGDAFIRLVKMIIAPVIFLTVAT 69

Query: 73  GIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVAT 132
           GIAGM+DL KVGRVAGKAM+YFL FSTLAL++GL+VANVVQPGAGM+IDPASLD  AVAT
Sbjct: 70  GIAGMTDLAKVGRVAGKAMIYFLAFSTLALVVGLVVANVVQPGAGMHIDPASLDAKAVAT 129

Query: 133 FAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLN 192
           +A KAHEQSI GFL NIIPTT+VGAFA+GDILQVLF SVLFGI+LA+VG+K E VV+FL 
Sbjct: 130 YAEKAHEQSITGFLMNIIPTTLVGAFAEGDILQVLFISVLFGISLAIVGKKAEPVVDFLQ 189

Query: 193 SLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLG 252
           +LT P+F+LVAILMKAAPIGAFGAMAFTIGKYG+ SIANLAMLIGTFY+TS LFVFIVLG
Sbjct: 190 ALTLPIFRLVAILMKAAPIGAFGAMAFTIGKYGIASIANLAMLIGTFYLTSFLFVFIVLG 249

Query: 253 AVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYS 312
           AVARYNGFSI++L+RYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYS
Sbjct: 250 AVARYNGFSILSLIRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYS 309

Query: 313 FNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLS 372
           FNLDGTNIYMTLAALFIAQAT   LS+GDQILLLLVAMLSSKGAAGITGAGFITLAATLS
Sbjct: 310 FNLDGTNIYMTLAALFIAQATDTPLSYGDQILLLLVAMLSSKGAAGITGAGFITLAATLS 369

Query: 373 VVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTVQLAAALGGQTG 432
           VVPSVPVAGMALILGIDRFMSECRALTN VGNAVATIVVA+WE ELD  QL+AALGG+  
Sbjct: 370 VVPSVPVAGMALILGIDRFMSECRALTNFVGNAVATIVVAKWEGELDQAQLSAALGGEAS 429

Query: 433 EDTSAAGLQPAE 444
            +   A +QPAE
Sbjct: 430 VEAIPAVVQPAE 441


Lambda     K      H
   0.324    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: 763
Number of extensions: 30
Number of successful extensions: 1
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: 444
Length of database: 441
Length adjustment: 32
Effective length of query: 412
Effective length of database: 409
Effective search space:   168508
Effective search space used:   168508
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