GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Herbaspirillum seropedicae SmR1

Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate HSERO_RS13105 HSERO_RS13105 C4-dicarboxylate ABC transporter

Query= SwissProt::P24943
         (421 letters)



>FitnessBrowser__HerbieS:HSERO_RS13105
          Length = 441

 Score =  343 bits (881), Expect = 5e-99
 Identities = 166/407 (40%), Positives = 265/407 (65%), Gaps = 9/407 (2%)

Query: 6   LAWQIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65
           L +Q+ + +++GI++G  +   P     ++P+GD F++LIKMI+ P++  ++V+G+A + 
Sbjct: 12  LYFQVLVAIVIGILLGHFY---PSTGEAMKPLGDGFVKLIKMIIAPVIFCTVVIGIAGME 68

Query: 66  DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMK--SLEKTDIQSYVDTTN 123
           D+KK+GK GG  ++YFE+++T+A+++GLL  N  QPG G+N+   SL+   I +Y   T 
Sbjct: 69  DMKKVGKTGGLALLYFEVVSTVALIIGLLLVNFLQPGVGMNVDPASLDTKSIAAY---TA 125

Query: 124 EVQHHSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183
             +  S+ +  + I+P ++ ++  KGD+L ++  +V+FG  +   G +G  V  F +  +
Sbjct: 126 PGKMGSVTDFVLGIIPTSMVDAFAKGDVLQVLLVAVLFGFALHKFGGRGTLVFDFIEKIS 185

Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVA 243
             +F V   IMK AP G F  +  T+ K+GV SL  L+KL+   Y T + FIFVVLG + 
Sbjct: 186 HVLFSVVGAIMKVAPIGAFGAMSFTIGKYGVGSLFSLAKLMGTFYLTCLLFIFVVLGIIT 245

Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNL 303
           +L G +I+  +K +K+EL++   T+SSE+VLP+++ KMEN G  K +   VIPTGYSFNL
Sbjct: 246 RLHGFSIWKFVKYIKEELLIVLGTSSSESVLPRMLAKMENAGAKKTVVGLVIPTGYSFNL 305

Query: 304 DGSTLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG 363
           DG+ +Y  +AA+FIAQ     M   Q+++LL VL++TSKG AG+ G  F+VL ATL  VG
Sbjct: 306 DGTAIYLTMAAVFIAQATNTPMTFVQELTLLGVLLLTSKGAAGITGSGFIVLAATLSAVG 365

Query: 364 -IPIEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409
            +P+ GLA I GIDR +  AR   N IGN +A ++++KW G+ + E+
Sbjct: 366 HVPVAGLALILGIDRFMSEARALTNTIGNGVATLVVAKWSGELDSER 412


Lambda     K      H
   0.326    0.143    0.404 

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: 435
Number of extensions: 21
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: 421
Length of database: 441
Length adjustment: 32
Effective length of query: 389
Effective length of database: 409
Effective search space:   159101
Effective search space used:   159101
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