GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citA in Magnetospirillum magneticum AMB-1

Align citrate transporter (characterized)
to candidate WP_083763475.1 AMB_RS08370 MFS transporter

Query= CharProtDB::CH_014606
         (431 letters)



>NCBI__GCF_000009985.1:WP_083763475.1
          Length = 445

 Score =  227 bits (579), Expect = 5e-64
 Identities = 137/413 (33%), Positives = 222/413 (53%), Gaps = 21/413 (5%)

Query: 10  TFGAILRV---TSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMR 66
           T G IL V   + GN +E +D++++  ++ Y +K FFP +     L+ T A+F  GF MR
Sbjct: 24  TKGKILMVFKGSVGNLVEYYDWYVYSAFSLYFSKYFFPGDDPTVQLLNTSAIFALGFFMR 83

Query: 67  PIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGF 126
           P+G  +LG + DR GR+  L++++++M  G+L+IA++PGY +IG+ AP+ +++ RLLQG 
Sbjct: 84  PLGGWLLGTHADRKGRKAALLVSVSMMCAGSLIIAVMPGYNSIGVAAPIALILARLLQGL 143

Query: 127 SAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGL-----NVTLGHDE 181
           S G E G  + YLSEIAT   +GFY+S+    Q V +++  L+  G+      V L   E
Sbjct: 144 SLGGEYGSAATYLSEIATKDRRGFYSSF----QYVTLIMGQLLALGVLMALQRVFLTTAE 199

Query: 182 ISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAGT 241
           +  WGWRIPF IG +   +   LR S++ETE+F   K           + ++ R +    
Sbjct: 200 LEAWGWRIPFVIGGLCAIVAIYLRSSMEETESFEHHKGDRVGESRIRALMRHPREVLTVI 259

Query: 242 LLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWL---PIGGAISDRI 298
            L    T  FY  T Y   Y       S  D+   TM+   + F+++   P+ G ISD++
Sbjct: 260 GLTMGGTVAFYTFTTYMQKYLVNTAGFSKSDA---TMISAAATFVYMLMHPLVGHISDKV 316

Query: 299 GRRPVLMGITLLALVTTLPVMNWLTAAPD-FTRMTLVLLWFSFFFGMYNGAMVAALTEVM 357
           GRR VL+   +++ + T+P++  L    D  T   LVL   +   G Y+        E+ 
Sbjct: 317 GRRAVLIAFGVMSTLCTVPILTALGQTHDSVTAFFLVLSGLTIVSG-YSAINAVVKAELF 375

Query: 358 PVYVRTVGFSLAFSLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGL 410
           PV +R +G  L F++  ++FGG    I+     + G+++   W++    LCGL
Sbjct: 376 PVQIRALGVGLPFAIGVSLFGGTAEYIALWFKSM-GNETWFYWYVTGCCLCGL 427


Lambda     K      H
   0.328    0.141    0.432 

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: 493
Number of extensions: 27
Number of successful extensions: 3
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: 431
Length of database: 445
Length adjustment: 32
Effective length of query: 399
Effective length of database: 413
Effective search space:   164787
Effective search space used:   164787
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 (21.8 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