Alignments for a candidate for dctM in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for dctM in Cupriavidus basilensis 4G11

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate RR42_RS06530 RR42_RS06530 C4-dicarboxylate ABC transporter

Query= SwissProt::Q9HU16
         (427 letters)



>FitnessBrowser__Cup4G11:RR42_RS06530
          Length = 434

 Score =  263 bits (672), Expect = 8e-75
 Identities = 149/428 (34%), Positives = 244/428 (57%), Gaps = 6/428 (1%)

Query: 4   LFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDS----VRSLAIKLFETSEHYTLLAI 59
           + LF++   LM +GVPI VSLGL G + I L + D+    + ++    +     Y LLAI
Sbjct: 6   IILFVVFLGLMMLGVPIGVSLGLGGLVAIGLSNLDTQMFGLLAVPQNFYAGLGKYPLLAI 65

Query: 60  PFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVG 119
           P F+L G+     GVA+RL+ FA A VG   G L + A+L  M    +SGS PA  AAVG
Sbjct: 66  PMFVLVGSIFDRSGVAQRLVTFAIAIVGRGPGMLPLVAILVAMFLGGISGSGPANAAAVG 125

Query: 120 SIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATE-TSVGKLFIAGVVPG 178
            + IA M R+GYP A+ A +V  A    ILIPPS+  ++Y+      SV  LF AG++PG
Sbjct: 126 GVMIAAMSRAGYPGAYSAAVVGAAAATDILIPPSVAFIIYSVLVPGASVPALFAAGMIPG 185

Query: 179 LLLGLILMVVIYIVARVKKLPAMPRVSLRE-WLASARKALWGLLLMVIILGGIYSGAFTP 237
           +L G+ L+V    +AR   + A+     R  +  S R+A WGL+   +ILGG+ +G FTP
Sbjct: 186 ILAGVALIVPAVWLARKHNMGAIEAGLPRPPFWKSLREAAWGLVAPFLILGGMRAGWFTP 245

Query: 238 TEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQI 297
           TEAA VA VY  FV + +YR + + +   +  E+ + + +++ ++A A +FA+ L+T  +
Sbjct: 246 TEAAVVAVVYGLFVGMVIYRSISMRDLFVIFQEAAETSAVILLVVALAGIFAYALSTLGV 305

Query: 298 PQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHL 357
              +A+ +   GL  +  L ++  +L+  G F++  +I LI  P+  PIA     +P+  
Sbjct: 306 IDPLANAIAHSGLGEYGVLALIVALLMTVGMFLDGISIFLIFVPLLLPIANAFHWNPVWF 365

Query: 358 GIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVS 417
           G+++ + + +G  TPP+ +NL V+  +  + +  T+   +  L+ + V +++V   P ++
Sbjct: 366 GVVLTLKVALGQFTPPLAVNLMVSCRIARVRMEETVPWVVWMLLAMFVAMLLVLAFPPLA 425

Query: 418 LALPNWLG 425
             LP++LG
Sbjct: 426 TWLPDYLG 433


Lambda     K      H
   0.330    0.144    0.425 

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: 595
Number of extensions: 34
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: 427
Length of database: 434
Length adjustment: 32
Effective length of query: 395
Effective length of database: 402
Effective search space:   158790
Effective search space used:   158790
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 (21.9 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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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