GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Shewanella oneidensis MR-1

Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate 201109 SO1948 sodium:dicarboxylate symporter family protein (NCBI ptt file)

Query= TCDB::P96603
         (421 letters)



>FitnessBrowser__MR1:201109
          Length = 437

 Score =  238 bits (608), Expect = 2e-67
 Identities = 133/413 (32%), Positives = 233/413 (56%), Gaps = 20/413 (4%)

Query: 3   LFKNLTVQVITAVIIGVIVGLVWPD--------VGKEMKPLGDTFINAVKMVIAPIIFFT 54
           L   + + + T +I G+I+  ++PD            +  +G  FI+++KM++ P++F +
Sbjct: 11  LTSKILIGMATGIIFGLILRNLFPDSIFIKDYITDGFLHVIGTIFISSLKMLVVPLVFIS 70

Query: 55  IVLGIAKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPG-AGLDYSKLEKGDV 113
           +V G   + +  K+G++GGK   ++   T LAL++ +F   I+ PG A L   KL     
Sbjct: 71  LVCGTCSLSEPSKLGRLGGKTLAFYLFTTVLALVLAVFAAVIVHPGDATLANEKLN---- 126

Query: 114 SQYTQNGGQGIDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVID 173
             Y     +   + + I  ++P+N V A ++G++LQ++ F+++FG  +A LGE+G  +  
Sbjct: 127 --YVAK--EAPSFAQVIIDMMPTNPVQAMSEGNMLQIIIFAVIFGFAIAHLGERGNRIAQ 182

Query: 174 FFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFV 233
            FD +++V  +++  +M+ AP G F  MA      GL++   +      V   + +  FV
Sbjct: 183 LFDDLNNVIMRVVTLVMQLAPYGVFALMAKLALTLGLETFGSVVKYFFLVLTLLLIHNFV 242

Query: 234 ALNIICKLY-GFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKME-RYGCSKSVVGLVI 291
             +I+ K + G +   ++R ++D  L    T+SS + LP  ++  E R G    +    +
Sbjct: 243 TYSILLKAFSGLNPLIFIRKMRDVQLFAFSTASSNATLPITIEASEHRLGVDNKIASFTL 302

Query: 292 PTGYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVL 351
           P G + N+DGT+I   +ATVF+AQVFG++LS+     +I+   L S G AGV G G I+L
Sbjct: 303 PLGATINMDGTAIMQGVATVFIAQVFGIELSLTDYAAVIVTATLASIGTAGVPGVGLIML 362

Query: 352 ASTLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDE 404
           A  L+ +  +P+EG+AL++GVDR +   R  VN+ G+ +AT+I+AKSE EF+E
Sbjct: 363 AMVLNQVG-LPVEGIALIIGVDRLLDMVRTAVNVTGDCVATVIIAKSEGEFNE 414


Lambda     K      H
   0.326    0.143    0.408 

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: 437
Number of extensions: 20
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: 421
Length of database: 437
Length adjustment: 32
Effective length of query: 389
Effective length of database: 405
Effective search space:   157545
Effective search space used:   157545
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 (21.6 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