GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cimH in Cupriavidus basilensis 4G11

Align L-malate/citrate:H+ symporter (electroneutral) (characterized)
to candidate RR42_RS29530 RR42_RS29530 malate permease

Query= TCDB::P94363
         (450 letters)



>FitnessBrowser__Cup4G11:RR42_RS29530
          Length = 451

 Score =  512 bits (1318), Expect = e-149
 Identities = 258/427 (60%), Positives = 329/427 (77%), Gaps = 6/427 (1%)

Query: 22  ENWFAKAMNIKVGIIPLPVYALLFILITVFVMHHDVKSDILTSIAVMAFFGFTFAQIGKS 81
           E W+ K M  ++GIIPLPVY +L  LI  F +   V  +I  +IAV+AFFGFT A+IGK 
Sbjct: 25  EGWW-KLMEFRIGIIPLPVYVILLALIAGFAVTGKVPGEISMAIAVLAFFGFTCAEIGKR 83

Query: 82  IPIVRSIGGPAILATFIPSAVVYYHLLPNDIVKSTTEFTENSNFLYLFIAGIVVGSILGM 141
           +PI+R+IG  AI ATFIPSA+ YYHLLP  I+  TTEFT+++NFLYLFIA I+VGSIL M
Sbjct: 84  LPIIRNIGAAAIFATFIPSALTYYHLLPKPILSLTTEFTKSTNFLYLFIASIIVGSILSM 143

Query: 142 KRETLVKAFMKIFIPLIVGSVTAAIVGLAVGTLLGLGFQHTLLYIVIPIMAGGVGEGAIP 201
            R  L++ F+KIFIPL VGS+ A IVG AVGT LGLG  HT  YIV+PIMAGGVGEGAIP
Sbjct: 144 DRRVLIQGFIKIFIPLAVGSIAAGIVGTAVGTALGLGAHHTFFYIVVPIMAGGVGEGAIP 203

Query: 202 LSIGYSDIMPISQGEAFALVLPSIMLGSLCAIILAGLLNRIGKKKPEWTGNGKVDRSEEE 261
           LSIGYS+I+ + QG+ FA VLP +MLGSL AIIL+G+L+++GK+ P  TG G++   EE+
Sbjct: 204 LSIGYSEILHLPQGDLFAQVLPPVMLGSLTAIILSGVLDKVGKRFPHLTGEGRLQVGEED 263

Query: 262 --SPALEESQSGQQMFNLSLFASGGILAVSLYLVGMLAHDFFGFPAPVAMLLLAVLIKLF 319
              P  EE +      +++  A+ GI A++LYL+G++  + FG PAPVAML LAVL+K+ 
Sbjct: 264 EMDPVQEEIRG---HIDVTHIAAAGITAITLYLLGLMCRNLFGLPAPVAMLFLAVLVKIT 320

Query: 320 RLVPASIENGAFGVSRFFSTAVTYPLLFAIGVSMTPWDKLVAAFNLSNIITILSVVVTMM 379
           R V   ++ GAF V +FFSTAVTYPLLFAIGV+MTPWDKL+AAF L+NI+TI++ V T+M
Sbjct: 321 RAVSPPLQEGAFVVYKFFSTAVTYPLLFAIGVAMTPWDKLIAAFTLANIVTIVATVTTLM 380

Query: 380 AVGFFTGKWLNMYPIETAIINACHSGQGGTGDVAILSAAERLELMPFAQVSTRIGGAITV 439
             GF   + L M+PI+TAI+NACHSGQGGTGDVAIL+AA R+ LMPFAQ++TRIGGAI V
Sbjct: 381 GTGFVVARMLKMHPIDTAIVNACHSGQGGTGDVAILTAANRMTLMPFAQIATRIGGAIVV 440

Query: 440 SLTLLLL 446
           +LTL++L
Sbjct: 441 TLTLIVL 447


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: 663
Number of extensions: 32
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