Alignments for a candidate for cimH in Cronobacter muytjensii ATCC 51329

GapMind for catabolism of small carbon sources

Alignments for a candidate for cimH in Cronobacter muytjensii ATCC 51329

Align L-malate/citrate:H+ symporter (electroneutral) (characterized)
to candidate WP_038867764.1 AFK63_RS01755 2-hydroxycarboxylate transporter family protein

Query= TCDB::P94363
         (450 letters)



>NCBI__GCF_001277195.1:WP_038867764.1
          Length = 454

 Score =  424 bits (1089), Expect = e-123
 Identities = 214/432 (49%), Positives = 306/432 (70%), Gaps = 5/432 (1%)

Query: 21  KENWFAKAMNIKVGIIPLPVYALLFILITVFVMHHDVKSDILTSIAVMAFFGFTFAQIGK 80
           KE W+    + K+GIIPLP++ L   LI +  +   + SDI+  +A +AFFGF   + GK
Sbjct: 23  KEKWWHIMDSWKIGIIPLPLFVLSGALIAIDCLGGKLPSDIVVMVATLAFFGFACGEFGK 82

Query: 81  SIPIVRSIGGPAILATFIPSAVVYYHLLPNDIVKSTTEFTENSNFLYLFIAGIVVGSILG 140
            +P++  +G  AI ATFIPSA+VYY  LP+ +V+STT+F +++N LYL+I  I+VGSI+ 
Sbjct: 83  RLPVIGKMGAAAICATFIPSALVYYGWLPDVVVESTTKFYKSTNILYLYICCIIVGSIMS 142

Query: 141 MKRETLVKAFMKIFIPLIVGSVTAAIVGLAVGTLLGLGFQHTLLYIVIPIMAGGVGEGAI 200
           M R TL++ F++IF P++ G V   +VG+ VG  LG+       ++++PIMAGGVGEGAI
Sbjct: 143 MNRTTLIQGFLRIFFPMLCGEVVGMLVGMGVGIALGMEPFQIFFFLILPIMAGGVGEGAI 202

Query: 201 PLSIGYSDIMPISQGEAFALVLPSIMLGSLCAIILAGLLNRIGKKKPEWTGNGKV--DRS 258
           PLSIGY+ ++ + QG A   VLP +MLGSL AII+AG LN++GK+ P  TG G++  DR 
Sbjct: 203 PLSIGYATLLHMDQGVALGRVLPIVMLGSLTAIIIAGCLNQLGKRYPHLTGEGELMPDRG 262

Query: 259 EE-ESPALEESQSGQQMFNLSLFASGGILAVSLYLVGMLAHDFFGFPAPVAMLLLAVLIK 317
           ++ ++  L  + SG+   +++  ASG +LAV LY++GML H   G PAPV ML +AV IK
Sbjct: 263 DKPQTQTLTTAFSGKA--DVTTIASGALLAVLLYMLGMLGHKVIGLPAPVGMLFIAVFIK 320

Query: 318 LFRLVPASIENGAFGVSRFFSTAVTYPLLFAIGVSMTPWDKLVAAFNLSNIITILSVVVT 377
           L   V   +  G+  V +FF T+VTYP+LFA+GV++TPW++L+ AF L+N++ I+S V  
Sbjct: 321 LVHGVSPRLLEGSQVVYKFFQTSVTYPILFAVGVAITPWEELMHAFTLNNLLVIVSTVSA 380

Query: 378 MMAVGFFTGKWLNMYPIETAIINACHSGQGGTGDVAILSAAERLELMPFAQVSTRIGGAI 437
           ++A GFF GK + M+PI+ AI++ C SGQGGTGDVAIL+A  R+ LMPFAQ++TRIGGAI
Sbjct: 381 LVATGFFVGKKIGMHPIDVAIVSCCQSGQGGTGDVAILTAGNRMTLMPFAQIATRIGGAI 440

Query: 438 TVSLTLLLLHQF 449
            VSL+LL+L  F
Sbjct: 441 NVSLSLLVLGNF 452


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: 661
Number of extensions: 25
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: 454
Length adjustment: 33
Effective length of query: 417
Effective length of database: 421
Effective search space:   175557
Effective search space used:   175557
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources