Alignments for a candidate for lacZ in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Cupriavidus basilensis 4G11

Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate RR42_RS26860 RR42_RS26860 beta-D-glucoside glucohydrolase

Query= SwissProt::E7CY69
         (757 letters)



>FitnessBrowser__Cup4G11:RR42_RS26860
          Length = 762

 Score =  246 bits (627), Expect = 4e-69
 Identities = 201/669 (30%), Positives = 299/669 (44%), Gaps = 95/669 (14%)

Query: 69  TCFPPAAGLSSSWNPELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSED 128
           T FP + GL+SSW+ E + +     A E   + + +   P V+I R+P  GR  E + ED
Sbjct: 112 TIFPISLGLASSWDMETVAQSARISAIEASADGLDMTFAPMVDISRDPRWGRTSEGFGED 171

Query: 129 PYLAGHEAIGIVEGVQSKGVGTS------LKHFAANNQ-ETDRLRVDARISPRALREIYF 181
           PYL    A   V G Q   +  +      +KHFA     E  R      +SP  + + Y 
Sbjct: 172 PYLVSLCAQASVRGFQGTSLANADSVMAVVKHFALYGAVEGGRDYNTVDMSPLRMYQDYL 231

Query: 182 PAFEHIVKKAQPWTIMCSYNRINGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGA------ 235
           P +   V  A    +M + N INGV +  N WLL D+LR  WGF GI +SD GA      
Sbjct: 232 PPYRAGVD-AGGGGVMIALNSINGVPATSNTWLLRDLLRKTWGFKGITVSDHGAIDELTK 290

Query: 236 -----DHDRGASL--NAGLNLEMPPSYTDDQIVYAVRDGLITPAQLDRMAQGMIDLVNKT 288
                D    A L   AG+++ M  S   D +   V+ G +    +D   + ++    K 
Sbjct: 291 HGVAKDARESAKLAITAGVDMSMHDSAYRDHLPELVKSGEVPMRVIDDAVREILGA--KY 348

Query: 289 RAAMSIDNYR---------FDVDA----HDEVAHQAAIESIVMLKNDDAILPLNAGPVAN 335
              +  D ++          DVDA    H E A  AA +S+V+L+N +  LPL       
Sbjct: 349 DLGLFQDPFKRIGAAEQDPADVDAPGRLHREAARAAARQSLVLLENRERTLPLKKSGT-- 406

Query: 336 PSATPQKIAVIGEFARTP-----RYQGGGSSHITPTKMTSFLDTLAERGIKADFAPGFTL 390
                  +AV+G  A  P      +   G S  T T +    D L   G +  +A G  +
Sbjct: 407 -------VAVVGPLADAPIDTMGSWSAAGKSGQTVTLLQGVRDALGGNG-RVAYARGANV 458

Query: 391 DLEP---------------------ADPALESEAVETAKNADVVLMFLGLPEAVESEGFD 429
             +                      A   + +EAV  A+ ADV+++ +G    +  E   
Sbjct: 459 TDDAGVVRYLNFMNWDKPEIVQDKRAPGDMIAEAVAAARGADVIVVAVGESRGMSHEASS 518

Query: 430 RDTLDMPAKQIALLEQVAAANQNVVVVLSNGSVITVAPWAK-NAKGILESWLLGQSGGPA 488
           R TL +P  Q  LL+ +    + +VVVL NG  +T+  W K NA  +LE+W  G  GG A
Sbjct: 519 RTTLSLPGSQETLLKALKTTGKPMVVVLMNGRPLTIN-WVKDNADAVLETWYAGTEGGHA 577

Query: 489 LADVIFGQVSPSGKLAQSIPLDINDDPSMLNW--------PGEEGHVDYGEGVFAGYRYY 540
           +ADV+FG  +PSGKL  S P  +   P+  N         PG+  +       +    + 
Sbjct: 578 IADVLFGDYNPSGKLPVSFPRSLGQIPTYYNQLRIGRPFVPGQPPN-------YTSQYFE 630

Query: 541 DTYGKAVDYPFGYGLSYATFEITGVAVAK---TGANTATVTATVTNTSDVDAAETVQVYV 597
           +T G    YPFGYGLSY  F ++G+ ++            + TV NT   D    VQ+Y+
Sbjct: 631 ETSGPL--YPFGYGLSYTDFGVSGITLSSPTMPRGGRIEASVTVKNTGQRDGETVVQLYI 688

Query: 598 VPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDERAFAYWSEKYNDWHVEAGEYAIEV 657
               A V RP  ELK F K  LKAGE + V   LDE    +++ K  ++  E GE+ +++
Sbjct: 689 QDVAASVVRPVKELKDFHKLMLKAGEERVVRFSLDEDKLKFFNAKL-EYAAEPGEFKVQI 747

Query: 658 GVSSRDIAD 666
           G+ S+ + +
Sbjct: 748 GLDSQAVRE 756


Lambda     K      H
   0.315    0.132    0.393 

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: 1334
Number of extensions: 73
Number of successful extensions: 6
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: 757
Length of database: 762
Length adjustment: 40
Effective length of query: 717
Effective length of database: 722
Effective search space:   517674
Effective search space used:   517674
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 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