GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Shewanella loihica PV-4

Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate 5209774 Shew_2227 sodium:dicarboxylate symporter (RefSeq)

Query= TCDB::P96603
         (421 letters)



>FitnessBrowser__PV4:5209774
          Length = 439

 Score =  234 bits (598), Expect = 3e-66
 Identities = 130/419 (31%), Positives = 232/419 (55%), Gaps = 34/419 (8%)

Query: 7   LTVQVITAVIIGVIVGLVWPDV--GKE----------MKPLGDTFINAVKMVIAPIIFFT 54
           LT +++  +  G++ GL+      G E          +  +G  FI++++M++ P++F +
Sbjct: 11  LTGKILIGMAGGILTGLLLRSFFPGSEFIEEYITNGLLNVVGSIFISSLQMLVVPLVFIS 70

Query: 55  IVLGIAKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPG------AGLDYSKL 108
           +V G   + D   +G++GGK   ++   T +AL + + V  ++ PG        + YS  
Sbjct: 71  LVCGTCSLSDPSSLGRLGGKTIAFYLFTTAIALSMAILVALLVHPGNASLAAENMQYSVK 130

Query: 109 EKGDVSQYTQNGGQGIDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKG 168
           E   +S             + + ++VP N + A  +G++LQ++ F+++FG  ++ +GE+G
Sbjct: 131 EAPSLS-------------DVLINLVPRNPIQAMTEGNMLQIIIFAVIFGFAISHIGERG 177

Query: 169 KSVIDFFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMF 228
           K V   F+ ++ V  +++  IM+ AP G F  M       GL++ + +    M V   + 
Sbjct: 178 KRVSALFNDLNEVIMRVVTLIMQLAPYGIFALMGKLALTLGLETFESVVKYFMVVLAVLL 237

Query: 229 LFVFVALNIICKLY-GFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKME-RYGCSKSV 286
           +  FV+  ++ KL+ G S + ++R ++D  L    T+SS + LP  ++  E R G    V
Sbjct: 238 VHAFVSYPVLLKLFSGLSPFTFIRKMRDVQLFAFSTASSNATLPVTLETSEHRLGVDNKV 297

Query: 287 VGLVIPTGYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGS 346
               +P G + N+DGT+I   +ATVF+AQVFG+DL+I     +++   L S G AGV G 
Sbjct: 298 ASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVVTATLASIGTAGVPGV 357

Query: 347 GFIVLASTLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEA 405
           G I+LA  L+ +  +P+EG+AL++GVDR +   R  VN+ G+ +AT+I+AKSEN F++A
Sbjct: 358 GLIMLAMVLNQVG-LPVEGIALIMGVDRLLDMVRTAVNVTGDSVATVIIAKSENAFNQA 415


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: 402
Number of extensions: 17
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: 439
Length adjustment: 32
Effective length of query: 389
Effective length of database: 407
Effective search space:   158323
Effective search space used:   158323
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