GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cimH in Klebsiella michiganensis M5al

Align L-malate/citrate:H+ symporter (electroneutral) (characterized)
to candidate BWI76_RS04555 BWI76_RS04555 citrate/acetate antiporter

Query= TCDB::P94363
         (450 letters)



>FitnessBrowser__Koxy:BWI76_RS04555
          Length = 451

 Score =  425 bits (1092), Expect = e-123
 Identities = 217/429 (50%), Positives = 298/429 (69%), Gaps = 2/429 (0%)

Query: 21  KENWFAKAMNIKVGIIPLPVYALLFILITVFVMHHDVKSDILTSIAVMAFFGFTFAQIGK 80
           K+ W+    N KVGIIPLP++ L   LI +  +   + SDI+  +A +AFFGF   + GK
Sbjct: 23  KQRWWHILDNWKVGIIPLPLFLLAGGLIALDCLGGKLPSDIVVMVATLAFFGFACGEFGK 82

Query: 81  SIPIVRSIGGPAILATFIPSAVVYYHLLPNDIVKSTTEFTENSNFLYLFIAGIVVGSILG 140
            +PI+  +G  AI ATFIPSA+V+Y LLP+ +V+STT+F +++N LYL+I  I+VGSI+ 
Sbjct: 83  RLPILGKLGAAAICATFIPSALVHYGLLPDVVVESTTKFYKSTNILYLYICCIIVGSIMS 142

Query: 141 MKRETLVKAFMKIFIPLIVGSVTAAIVGLAVGTLLGLGFQHTLLYIVIPIMAGGVGEGAI 200
           M R TL++ FM+IF P++ G +   +VG+ VGT LGL       +IV+PIMAGGVGEGAI
Sbjct: 143 MNRTTLIQGFMRIFFPMLCGEIVGMVVGVGVGTALGLEPFQVFFFIVLPIMAGGVGEGAI 202

Query: 201 PLSIGYSDIMPISQGEAFALVLPSIMLGSLCAIILAGLLNRIGKKKPEWTGNGKVDRSEE 260
           PLSIGY+ +M + QG A   VLP +MLGSL AI++AG LN++GK+ P  TG G++  +  
Sbjct: 203 PLSIGYAALMHMDQGVALGRVLPMVMLGSLTAIVIAGGLNQLGKRFPHLTGEGQLMPNRR 262

Query: 261 ESPALEESQSGQQMFNLSLFASGGILAVSLYLVGMLAHDFFGFPAPVAMLLLAVLIKLFR 320
                E    G+   +++  ASG +LAV LY++GML     G PAPV ML LAVL+KL  
Sbjct: 263 NETHRETPAEGK--MDVTTLASGALLAVLLYMLGMLGQKTIGLPAPVGMLFLAVLLKLVN 320

Query: 321 LVPASIENGAFGVSRFFSTAVTYPLLFAIGVSMTPWDKLVAAFNLSNIITILSVVVTMMA 380
            V   ++ G+  V +FF TAVTYP+LFA+GV++TPW +LV AF L+N++ I+S V  ++A
Sbjct: 321 GVSPRLQEGSQMVYKFFRTAVTYPILFAVGVAITPWQELVNAFTLTNLLVIISTVSALVA 380

Query: 381 VGFFTGKWLNMYPIETAIINACHSGQGGTGDVAILSAAERLELMPFAQVSTRIGGAITVS 440
            GF  GK + M+PI+ AI++ C SGQGGTGDVAIL++  R+ LMPFAQ++TRIGGAI VS
Sbjct: 381 TGFLVGKKIGMHPIDVAIVSCCQSGQGGTGDVAILTSGNRMNLMPFAQIATRIGGAINVS 440

Query: 441 LTLLLLHQF 449
           L LL L  F
Sbjct: 441 LGLLFLSHF 449


Lambda     K      H
   0.326    0.141    0.412 

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: 672
Number of extensions: 44
Number of successful extensions: 2
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: 450
Length of database: 451
Length adjustment: 33
Effective length of query: 417
Effective length of database: 418
Effective search space:   174306
Effective search space used:   174306
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