GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Klebsiella michiganensis M5al

Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate BWI76_RS26760 BWI76_RS26760 C4-dicarboxylate transporter DctA

Query= CharProtDB::CH_088342
         (421 letters)



>FitnessBrowser__Koxy:BWI76_RS26760
          Length = 428

 Score =  338 bits (867), Expect = 2e-97
 Identities = 154/402 (38%), Positives = 266/402 (66%), Gaps = 5/402 (1%)

Query: 9   QIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68
           Q+   + +GI++G  +   P++ A ++P+GD F++LIKMI+ P++  ++V G+A +  +K
Sbjct: 12  QVLSAIAIGILLGHFY---PELGAQMKPLGDAFVKLIKMIIAPVIFCTVVTGIAGMESMK 68

Query: 69  KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEVQHH 128
            +G+ G   ++YFEI++TIA+++GL+  N+ QPGAG+N+      D ++      + +  
Sbjct: 69  AVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPAT-LDAKAVAVYAEQAKDQ 127

Query: 129 SMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFY 188
            +V   ++I+P ++  + ++G++L ++ F+V+FG  +  +G KG+ +    +  ++ +F 
Sbjct: 128 GIVAFLLDIIPGSVIGAFASGNILQVLMFAVLFGFALHRLGSKGQLIFNVIESFSQVIFG 187

Query: 189 VTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKLFGI 248
           + N IM+ AP G F  +  T+ K+GV +L+ L +L++  Y T + F+  VLG +AK  G 
Sbjct: 188 IINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIVCFYITCILFVVVVLGSIAKATGF 247

Query: 249 NIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGSTL 308
           +IF  I+ +++EL++   T+SSE+ LPR++DKMEK GC K++   VIPTGYSFNLDG+++
Sbjct: 248 SIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTSI 307

Query: 309 YQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG-IPVE 367
           Y  +AA+FIAQ     M +  QI+LL+VL+++SKG AGV G  F+VL AT+  VG +PV 
Sbjct: 308 YLTMAAVFIAQATNSHMDIFHQITLLVVLLLSSKGAAGVTGSGFIVLAATISAVGHLPVA 367

Query: 368 GLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409
           GLA I GIDR +  AR   N++GN +A I+++KW  + + ++
Sbjct: 368 GLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDSQQ 409


Lambda     K      H
   0.326    0.143    0.402 

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: 412
Number of extensions: 17
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: 428
Length adjustment: 32
Effective length of query: 389
Effective length of database: 396
Effective search space:   154044
Effective search space used:   154044
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