Alignments for a candidate for lacZ in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Caulobacter crescentus NA1000

Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate CCNA_01019 CCNA_01019 beta-glucosidase

Query= SwissProt::E7CY69
         (757 letters)



>FitnessBrowser__Caulo:CCNA_01019
          Length = 758

 Score =  326 bits (836), Expect = 2e-93
 Identities = 221/681 (32%), Positives = 333/681 (48%), Gaps = 56/681 (8%)

Query: 24  GDAWHLQGVESKGIPSYMITDGPHGLRKSLASSAGETDLDDSVPATCFPPAAGLSSSWNP 83
           G A ++ GV   GIP+   TD   G+       A +    +    T  P     +++WNP
Sbjct: 90  GSAGYIAGVPRLGIPAQFQTDAGVGV-------ATQGSAKEFRERTALPSGMATTATWNP 142

Query: 84  ELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSEDPYLAGHEAIGIVEGV 143
           EL  + G  + +E       V L  GVN+ R P  GR FEY  EDP LAG      + G+
Sbjct: 143 ELAFQGGAMIGKEARDSGFNVQLAGGVNLVREPRNGRNFEYGGEDPLLAGVMVAAQIRGI 202

Query: 144 QSKGVGTSLKHFAANNQETDRLRVDARISPRALREIYFPAFEHIVKKAQPWTIMCSYNRI 203
           QS  + +++KH+A N QET R  V + I   A R     AF+  ++++ P ++MC+YNR+
Sbjct: 203 QSNNIISTIKHYALNAQETGRFVVSSNIDDTAARMSDLLAFQFAIEQSDPHSVMCAYNRV 262

Query: 204 NGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGADHDRGASLNAGLNLEMPPSYTDDQIVYA 263
           N V++ ++ WLL  VL+ +WG+ G VMSDWGA H    + NAGL+ E      D Q  +A
Sbjct: 263 NSVYACESDWLLNTVLKKDWGYKGYVMSDWGAAHSSAKAANAGLDQESAGDAFDKQPFFA 322

Query: 264 ------VRDGLITPAQLDRMAQGMI------DLVNKTRAAMSIDNYRFDVDAHDEVAHQA 311
                 +  G ++ A++D MA+ ++       +V+       +      + AH ++    
Sbjct: 323 APLKADLASGAVSQARIDDMARRVLRAMFASGVVDHPLTGAPLAMPAETLAAHAKITQAD 382

Query: 312 AIESIVMLKNDDAILPLNAGPVANPSATPQKIAVIGEFARTPRYQGGGSSHITPTKMTS- 370
           A E IV+LKND  +LPL        + T + IAVIG +A      GGGSS + P    + 
Sbjct: 383 AEEGIVLLKNDGGLLPL--------AKTAKTIAVIGSYADVGVLSGGGSSQVYPVGGRAV 434

Query: 371 -------------FLDTLAERGIKADFAPGFTLDLEPADPALESEAVETAKNADVVLMFL 417
                        +  +   + I A +     +  +  DPA    A + A ++D+ L+F 
Sbjct: 435 QGLEPKTWPGPVIYYPSSPLKAIAARYPGAKVVYDDGTDPA---RAAKLAASSDLALVF- 490

Query: 418 GLPEAVESEGFDRDTLDMPAKQIALLEQVAAANQNVVVVLSNGSVITVAPWAKNAKGILE 477
              +   +E  D  TL++P  Q A ++ VA+AN+  VVVL  G  + + PW      ++E
Sbjct: 491 --ADQWTTESVDVTTLNLPKNQDATIDAVASANKKTVVVLLTGGPL-LMPWLDKVGAVVE 547

Query: 478 SWLLGQSGGPALADVIFGQVSPSGKLAQSIPLDINDDP----SMLNWP-GEEGHVDYG-E 531
           +W  G +GG A+A V+ G+V  SG+L  + P  + + P      L  P GE   VDY  E
Sbjct: 548 AWFPGTAGGEAIARVLTGEVDASGRLPVTFPKSVAELPRPKLDGLGKPDGEMFDVDYTLE 607

Query: 532 GVFAGYRYYDTYGKAVDYPFGYGLSYATFEITGVAVAKTGANTATVTATVTNTSDVDAAE 591
           G   GY++YD       + FG+GLSY  F  + +  + +G +T TV+  V N       +
Sbjct: 608 GAAVGYKWYDLKKIEPLFAFGHGLSYTQFAYSNLTASASG-DTLTVSFEVKNVGRRPGKD 666

Query: 592 TVQVYVVPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDERAFAYWSEKYNDWHVEAG 651
             QVYV P       PK  L GF K  L  G S+ V + +D R  A W  K + W + AG
Sbjct: 667 VPQVYVGPKAGGWEAPK-RLAGFQKVSLAPGASQRVTVTVDPRLLAVWDSKAHGWSIAAG 725

Query: 652 EYAIEVGVSSRDIADTVAVAL 672
           +Y I +G SSR I+ T  V L
Sbjct: 726 QYDIALGASSRAISSTAQVTL 746


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: 1351
Number of extensions: 65
Number of successful extensions: 8
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: 758
Length adjustment: 40
Effective length of query: 717
Effective length of database: 718
Effective search space:   514806
Effective search space used:   514806
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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Protein sequences (fasta format)
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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