Alignments for a candidate for araVsh in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Cupriavidus basilensis 4G11

Align ABC transporter related (characterized, see rationale)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Cup4G11:RR42_RS30800
          Length = 530

 Score =  265 bits (677), Expect = 3e-75
 Identities = 165/484 (34%), Positives = 265/484 (54%), Gaps = 15/484 (3%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           IL L  I+K +  + A +D+SL L  GEV ALLGENGAGKSTLV ++ G    D G +  
Sbjct: 5   ILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEV 64

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G+P     P  A  AGI  V+Q   L  NL+V  N+ LG +P     +          A
Sbjct: 65  DGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKVLA 124

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           +  +F L +   A + + S+  +Q + I + +   A+VL+LDEPTA L   E + LF  L
Sbjct: 125 LAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTL 184

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR--SL 241
            QL A+G++++FI+H LD+V ++SDRI VLR G+ +     A+  + +L E M+GR  ++
Sbjct: 185 AQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVVAM 244

Query: 242 QEQLVDKQEKERTVTRAEAVLLSLEDVSVKGS-----IQSMNLTVPKGQAVGLAGLLGSG 296
            E++  +  ++     A   +L+LE V  + +     ++ ++L V  G+ VG+AG+ G+G
Sbjct: 245 PERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSGNG 304

Query: 297 RSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIREN 356
           ++ +     G+     G I LAG+ ++ ++P   I AG+A  PEDR   G++G L++ EN
Sbjct: 305 QAALAELASGMLEASEGRITLAGKPMS-AKPRAWIGAGVARVPEDRHAIGVVGDLAVWEN 363

Query: 357 II--LALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARW 414
            +     + R   W  +     Q  A+  + +  + T   D P   +SGGN QK+IL R 
Sbjct: 364 AVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILGRA 423

Query: 415 LAIE-----PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNK 469
           L++      P L+V  +PT G+DIGA A +   +     EG ++L+ S +LDEL A +++
Sbjct: 424 LSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALADR 483

Query: 470 VVVL 473
           + V+
Sbjct: 484 IAVM 487



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 56/218 (25%), Positives = 113/218 (51%), Gaps = 6/218 (2%)

Query: 277 MNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIA 336
           ++L + +G+ + L G  G+G+S + + +FG  + D+G++ + GQ L   QP  A++AGI 
Sbjct: 24  ISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPGQPRAALTAGIG 83

Query: 337 LCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADK 396
           +  +   +      LS+ +NI+L  Q  +  WR   +  + ++     ++  +A     +
Sbjct: 84  MVHQHFTL---ADNLSVLDNIMLGTQP-LWQWRLDGHAARGKVLAL-AERFGLAVRPQAR 138

Query: 397 PIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVA 456
            + +LS G +Q+V + + L     +L+LDEPT  +       +   +  L  EG+S++  
Sbjct: 139 -VGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTLAQLIAEGLSVIFI 197

Query: 457 SSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQ 494
           S +LDE++  S+++ VLR    V   + A+ T   + +
Sbjct: 198 SHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAE 235



 Score = 63.9 bits (154), Expect = 1e-14
 Identities = 64/236 (27%), Positives = 109/236 (46%), Gaps = 14/236 (5%)

Query: 16  GVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMD 75
           G   L +VSL++ AGE+  + G +G G++ L ++ +G      G I   G+P     P  
Sbjct: 278 GRALLREVSLQVRAGEIVGIAGVSGNGQAALAELASGMLEASEGRITLAGKPMSAK-PRA 336

Query: 76  AQKAGISTVYQE---VNLVPNLTVAQNLFLGY--EPR--RLGLIHFKKMYADARAVLTQF 128
              AG++ V ++   + +V +L V +N       EPR  R G+I        AR ++ +F
Sbjct: 337 WIGAGVARVPEDRHAIGVVGDLAVWENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARF 396

Query: 129 KL---DIDVSAPLSDYSIAVQQLIAIA---RGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182
            +    IDV A         + ++  A   RG   + +++V  +PT  LD   V  +   
Sbjct: 397 DVRTAGIDVPARTMSGGNMQKLILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRAR 456

Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG 238
           L     +G A++ I+  LD+++ ++DRI V+  G       TA     +L  AM G
Sbjct: 457 LLDAAREGAAVLLISEDLDELHALADRIAVMHAGHLTEARPTAAWTLGELGLAMAG 512


Lambda     K      H
   0.319    0.136    0.377 

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: 658
Number of extensions: 30
Number of successful extensions: 10
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: 499
Length of database: 530
Length adjustment: 35
Effective length of query: 464
Effective length of database: 495
Effective search space:   229680
Effective search space used:   229680
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)
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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