GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Cupriavidus basilensis 4G11

Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate RR42_RS33745 RR42_RS33745 C4-dicarboxylate transporter

Query= SwissProt::P24943
         (421 letters)



>FitnessBrowser__Cup4G11:RR42_RS33745
          Length = 452

 Score =  327 bits (839), Expect = 3e-94
 Identities = 153/402 (38%), Positives = 256/402 (63%), Gaps = 5/402 (1%)

Query: 9   QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68
           Q+ I +  GI++G      P + + L+P+GDIF+RLIKM+  PI+ +++V+G+A +  +K
Sbjct: 12  QVLIAVAAGILLGIFM---PHIGSALKPLGDIFIRLIKMVFAPIIFATVVLGIAKMESMK 68

Query: 69  KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMKSLEKTDIQSYVDTTNEVQHH 128
            LG++G + ++YFE+++T A+++G++  N+ QPG G+N+      D +S    T +V+H 
Sbjct: 69  DLGRVGWRALLYFEVLSTFALLLGVIVVNVVQPGHGMNVDPAT-LDTKSIAAYTAQVKHE 127

Query: 129 SMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFY 188
            +++  +N+VP +I ++L K D+L I+ FSV  G+ +A +GE+GKP +      A AMF 
Sbjct: 128 GIMDFLLNLVPMSIMDALAKNDILQILVFSVFMGVALAHLGERGKPFVAALDSFANAMFA 187

Query: 189 VTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKLFGI 248
           +   IM+ AP   F  +  TV K+G  S+  L KLV  +Y T   F+ +VLG + ++ G 
Sbjct: 188 IVGMIMRVAPVAAFGAMSFTVGKYGFGSIASLGKLVATMYGTCALFVLIVLGAICRICGF 247

Query: 249 NIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDGSTL 308
            +F+ +K +KDE++    T+SSE+V+P++M K+EN G  K +   V+P G +FN DG  +
Sbjct: 248 GLFNFLKYIKDEILTVLGTSSSESVIPQLMRKLENVGVSKPVVGLVVPAGLTFNPDGQCI 307

Query: 309 YQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG-IPIE 367
           Y  +AAIFIAQ     + ++ Q  +L VL++TSKG AG+ G  F+ L ATL ++G IP+ 
Sbjct: 308 YYTMAAIFIAQATNTPLTLTDQFVVLGVLLLTSKGSAGITGSGFITLAATLASLGKIPVA 367

Query: 368 GLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409
           G+  + G+DR +  AR   N IGN++A + ++KW G  +E++
Sbjct: 368 GMVLLLGVDRFMSEARAITNTIGNAVATMAIAKWVGALDEDR 409


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: 439
Number of extensions: 30
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: 452
Length adjustment: 32
Effective length of query: 389
Effective length of database: 420
Effective search space:   163380
Effective search space used:   163380
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