Alignments for a candidate for H281DRAFT_01113 in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Cupriavidus basilensis 4G11

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Cup4G11:RR42_RS03360
          Length = 537

 Score =  301 bits (770), Expect = 5e-86
 Identities = 191/504 (37%), Positives = 282/504 (55%), Gaps = 22/504 (4%)

Query: 6   VSSAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQ 65
           +S      P L +  + K F GV ALR V L+   G+++ L+GENG GKSTL+KI+SGA 
Sbjct: 1   MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 60

Query: 66  PPDEG-QLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRL 124
             D G +  I+G          A   G+  +YQ+LSL PN+SVAEN+ L   L    G +
Sbjct: 61  TADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQ-RRGLV 119

Query: 125 ARTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMD 184
           AR    R  A T AR        G     +  +  L +A RQLV IARA+  EA+ ++MD
Sbjct: 120 ARGDMVRACAPTLARL-------GADFSPAANVASLSIAQRQLVEIARAVHFEARILVMD 172

Query: 185 EPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIA 244
           EPTT L+  E D L A++  LR +G+ +L++SH++ E   +   V VLRDG  +     A
Sbjct: 173 EPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRA 232

Query: 245 EFTKAQISELMTGRHLSNERYRESAHA--QDIVLDVRGFTRAGQFSDVSFKLHGGEILGV 302
             ++A + ++M GR LS    +    A  ++++L VR      +    SF L  GE+LG+
Sbjct: 233 HLSQAALVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGL 292

Query: 303 TGLLDSGRNELARALAGVAPAQSGDVLL-----DGQQIALRT--PSDAKRHRIGYVPEDR 355
            GL+ +GR ELAR + G      G+V +      G  + L    P  A    I Y+ EDR
Sbjct: 293 AGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDR 352

Query: 356 LNEGLFLDKPIRDNVITAMISSLRDRFG--QIDRTRAQALAEQTVKELQIATPGVDKPVQ 413
             +GLFLD+ + +N+   +I + RD  G  +++RT A+    + +  L I        V 
Sbjct: 353 KLQGLFLDQSVHENI--NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVG 410

Query: 414 SLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDD 473
           +LSGGNQQ+V++ R L I PRVLIL  PT GVD+G+K  IYR++  L+Q G+ I++IS +
Sbjct: 411 ALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSE 470

Query: 474 LPELLQNCDRILMMKKGHVSAEYR 497
           LPE++  CDR+L+M++G ++ E R
Sbjct: 471 LPEVVGLCDRVLVMREGTLAGEVR 494



 Score = 58.2 bits (139), Expect = 8e-13
 Identities = 51/222 (22%), Positives = 98/222 (44%), Gaps = 16/222 (7%)

Query: 290 VSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQ-SGDVLLDGQQIALRTPSDAKRHRI 348
           V    + GE+  + G   +G++ L + L+G   A   G+  +DGQ++ +  P  A+   +
Sbjct: 29  VELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGV 88

Query: 349 GYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGV 408
             + ++     L  +  + +N+        R    + D  RA A          +A  G 
Sbjct: 89  AVIYQEL---SLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPT--------LARLGA 137

Query: 409 D----KPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRG 464
           D      V SLS   +Q V I R +  + R+L++  PT  +     D ++ ++++L   G
Sbjct: 138 DFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEG 197

Query: 465 IGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADL 506
           + I+ IS  + E+ +  DR+ +++ G          LS+A L
Sbjct: 198 MAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAAL 239


Lambda     K      H
   0.319    0.135    0.376 

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: 637
Number of extensions: 35
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 515
Length of database: 537
Length adjustment: 35
Effective length of query: 480
Effective length of database: 502
Effective search space:   240960
Effective search space used:   240960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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:

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
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