Alignments for a candidate for BPHYT_RS16930 in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Cupriavidus basilensis 4G11

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Cup4G11:RR42_RS30800
          Length = 530

 Score =  241 bits (614), Expect = 6e-68
 Identities = 164/491 (33%), Positives = 251/491 (51%), Gaps = 22/491 (4%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           LR   I K F  + A D +S ++  G+V  L+GENGAGKSTL+ IL G Y  D+G V +D
Sbjct: 6   LRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVD 65

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124
           G  +      +++ AGI ++HQ      +L+V +N++LG  P     ++   A+  V   
Sbjct: 66  GQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKVLAL 125

Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184
            E  G+A+ P A++ +LS+ +RQ VEI KAL R ARV+ LDEPT+ L+  E E LF  + 
Sbjct: 126 AERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTLA 185

Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS- 243
            L A+  ++I+ISH++DE+  + D   + R G+ +A     +  T+  +   MVGR ++ 
Sbjct: 186 QLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQ-TTKAELAELMVGRVVAM 244

Query: 244 ----------DIYNYSARP--LGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAG 291
                     D  N +A P  L      A+   G AL +  S +VR GEIVG  G+ G G
Sbjct: 245 PERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSGNG 304

Query: 292 RSELMHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSEN 351
           ++ L  L  G      G + L GKP+  +     I  G+   PEDR   G+V    V EN
Sbjct: 305 QAALAELASGMLEASEGRITLAGKPMSAKPRA-WIGAGVARVPEDRHAIGVVGDLAVWEN 363

Query: 352 I--NISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSR 409
                     + R G+ + R      A   +    ++T       R +SGGN QK IL R
Sbjct: 364 AVSEQLSEPRFSRWGV-IRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILGR 422

Query: 410 WLA----EPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSD 465
            L+        ++V+  +PT G+D+GA   +   +   A  G A+++IS +L E+  ++D
Sbjct: 423 ALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALAD 482

Query: 466 RIVVMRQGRIS 476
           RI VM  G ++
Sbjct: 483 RIAVMHAGHLT 493



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 61/221 (27%), Positives = 109/221 (49%), Gaps = 10/221 (4%)

Query: 273 SFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVL 332
           S E++RGE++   G  GAG+S L+ +++G      G + +DG+P+       A+  GI +
Sbjct: 25  SLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPGQPRAALTAGIGM 84

Query: 333 CPEDRKEEGIVAMATVSENINISCRRHYL-RVGMFLDRKKEAETADRFIKLLKIKTPSRR 391
                +   +    +V +NI +  +  +  R+     R K    A+RF   L ++  +R 
Sbjct: 85  V---HQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKVLALAERFG--LAVRPQAR- 138

Query: 392 QKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIV 451
             +  LS G +Q+  + + L     +V+ILDEPT  +       +++ + QL   G +++
Sbjct: 139 --VGELSVGERQRVEIVKALYR-GARVLILDEPTAVLTPHEAETLFSTLAQLIAEGLSVI 195

Query: 452 MISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSL 492
            IS +L EVL VSDRI V+R G++         T+  +  L
Sbjct: 196 FISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAEL 236



 Score = 63.5 bits (153), Expect = 2e-14
 Identities = 59/230 (25%), Positives = 101/230 (43%), Gaps = 24/230 (10%)

Query: 16  GVRALDG------VSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEVR 69
           G RA +G      VS  V  G++ G+ G +G G++ L ++  G  +   GR+ + G  + 
Sbjct: 272 GARAANGRALLREVSLQVRAGEIVGIAGVSGNGQAALAELASGMLEASEGRITLAGKPMS 331

Query: 70  FTSAASSIAAGIAVIHQE---LQYVPDLTVAENLLLGQL--PNSLGW--VNKREAKRFVR 122
               A  I AG+A + ++   +  V DL V EN +  QL  P    W  + +  A+RF R
Sbjct: 332 AKPRAW-IGAGVARVPEDRHAIGVVGDLAVWENAVSEQLSEPRFSRWGVIRRAAAQRFAR 390

Query: 123 E---RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNA-----RVIALDEPTSSLSHR 174
           +   R +     +D  A  R +S    Q + + +AL         R++   +PT  L   
Sbjct: 391 DLVARFDVRTAGIDVPA--RTMSGGNMQKLILGRALSVRGEGSAPRLVVASQPTWGLDIG 448

Query: 175 ETEVLFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPT 224
               +   + D   +  A++ IS  +DE++ L D   +   G    + PT
Sbjct: 449 AVAYVRARLLDAAREGAAVLLISEDLDELHALADRIAVMHAGHLTEARPT 498


Lambda     K      H
   0.320    0.136    0.385 

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: 648
Number of extensions: 36
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 512
Length of database: 530
Length adjustment: 35
Effective length of query: 477
Effective length of database: 495
Effective search space:   236115
Effective search space used:   236115
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 (21.8 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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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 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