Alignments for a candidate for lacZ in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Paraburkholderia phymatum STM815

Align β-galactosidase (A4-β-Gal) (EC 3.2.1.23) (characterized)
to candidate WP_012401732.1 BPHY_RS11950 beta-galactosidase

Query= CAZy::BAA28362.1
         (645 letters)



>NCBI__GCF_000020045.1:WP_012401732.1
          Length = 660

 Score =  679 bits (1751), Expect = 0.0
 Identities = 334/655 (50%), Positives = 430/655 (65%), Gaps = 14/655 (2%)

Query: 2   LGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLA 61
           LGVCYYPEHWP+  W++DARRM+  G+  VRI EFAW+ +EP PG  +WGWLD A+  L 
Sbjct: 3   LGVCYYPEHWPESMWEDDARRMKALGIEQVRIAEFAWSRMEPTPGEYDWGWLDRAVDVLG 62

Query: 62  AEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121
             GL+VV+ TPTATPPKWL+DR+P+ILPV  +GR R FG RRHY FSSP Y E +R+I T
Sbjct: 63  KAGLQVVMCTPTATPPKWLIDRHPDILPVGADGRPRAFGSRRHYDFSSPSYFEASRKICT 122

Query: 122 LLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAF 181
            +A RYG   AVA +QTDNE+GCH+TV  Y P     FR WL+ARY TI+ALN AWGT F
Sbjct: 123 AVAGRYGKHPAVAYWQTDNEFGCHNTVVSYSPAAVARFREWLKARYQTIDALNRAWGTVF 182

Query: 182 WSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTHN 241
           WS  YRSF E++ P  TV E +PSH LDY RFASD+V  +NR+QVEI+RAH+PG+ V HN
Sbjct: 183 WSMEYRSFDEIDAPIATVTEAHPSHRLDYRRFASDEVARYNRMQVEIIRAHSPGRPVAHN 242

Query: 242 FMGFFTDLDAFALAQDLDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAFHHDLYR 301
           FM  FT+ D + +A+DLD A+WDSYPLG  +     PE K ++ RTGHPD A+F+HD+YR
Sbjct: 243 FMQLFTEFDHYKVARDLDVATWDSYPLGALEEQWYAPEIKAKFLRTGHPDFASFNHDVYR 302

Query: 302 GVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQEQ 361
           G+ +  FWVMEQQPGPVNWA  NPSP PGMVRLW+WEA AHGA  VSYFRWRQAPFAQEQ
Sbjct: 303 GMSKLPFWVMEQQPGPVNWAHWNPSPLPGMVRLWSWEAFAHGAGCVSYFRWRQAPFAQEQ 362

Query: 362 MHAGLHRPDSAPDQGFFEAKRVAEELAALALPPV-----AQAPVALVFDYEAAWIYEVQP 416
           MHAGL+ PD+  D G  EA++VA E+A ++          ++ +AL++DYEA W++E+ P
Sbjct: 363 MHAGLNTPDNRLDVGGSEAQKVAHEIAQVSSANADADANVRSKIALIYDYEAKWLFEIHP 422

Query: 417 QGAEWSYLGLVYLFYSALRRLGLDVDVVPPGASLRGYAFAVVPSLPIVREEALEAFREAE 476
           QGA++ Y    + +YSALR LG DVDV+   A   GY   VVP LP+V ++       + 
Sbjct: 423 QGADFHYPRFAFEYYSALRALGFDVDVIAADAPFDGYKMIVVPPLPVVPDDFAVRLAASG 482

Query: 477 GPVLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLEV-----AEGALGR 531
             ++ GPR+GSKT   QIP  LPPG L +LLP++V RVES+ P + E      A   L  
Sbjct: 483 AQIVLGPRTGSKTADLQIPPNLPPGALASLLPIRVWRVESMRPNVTEPVHMNGAGDGLHE 542

Query: 532 FPLGLWREWVEAP----LKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAAEA 587
                WR+ ++A           F DG  A  + G   Y A+     L   L   +A EA
Sbjct: 543 GHARHWRDLIDAADERGFDVRARFDDGHPAYVQHGCVHYFASLFDDALTQALFGRIATEA 602

Query: 588 GLKVLSLPEGLRLRRRGTWVFAFNYGPEAVEAPASEGARFLLGSRRVGPYDLAVW 642
           GL    L + +R+ RRG   + FNY          + +RF++G+R V P  ++ +
Sbjct: 603 GLTPTLLGDSVRISRRGKLAYVFNYANAPHTIEGVDASRFVIGTREVEPQGVSAY 657


Lambda     K      H
   0.322    0.139    0.454 

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: 1440
Number of extensions: 82
Number of successful extensions: 4
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: 645
Length of database: 660
Length adjustment: 38
Effective length of query: 607
Effective length of database: 622
Effective search space:   377554
Effective search space used:   377554
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 (21.9 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
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