Alignments for a candidate for lacZ in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Paraburkholderia bryophila 376MFSha3.1

Align β-galactosidase (A4-β-Gal) (EC 3.2.1.23) (characterized)
to candidate H281DRAFT_02633 H281DRAFT_02633 beta-galactosidase

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



>FitnessBrowser__Burk376:H281DRAFT_02633
          Length = 657

 Score =  699 bits (1803), Expect = 0.0
 Identities = 348/656 (53%), Positives = 432/656 (65%), Gaps = 13/656 (1%)

Query: 2   LGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLA 61
           LGVCYYPE WP   W +DARRM + G++HVRI EFAW+ +EP  G  EW WLD AI TLA
Sbjct: 3   LGVCYYPEQWPDTMWADDARRMVDMGITHVRIAEFAWSRMEPRAGVYEWAWLDRAIDTLA 62

Query: 62  AEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121
             GLK+VLGTPTA+PP+WLV+  P++LPV  +G    +G RRHY   S  YR E  RI  
Sbjct: 63  GAGLKIVLGTPTASPPRWLVEAIPDMLPVRADGTTWNYGSRRHYDICSEPYRRECVRITE 122

Query: 122 LLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAF 181
            +A RYG   AV  +QTDNE GCH+TV  Y    ++ FRGWL  RY T+  LN  WG  F
Sbjct: 123 AMAARYGAHPAVVAWQTDNELGCHETVPSYSNAARQRFRGWLARRYETVGELNTRWGNVF 182

Query: 182 WSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTHN 241
           WS  Y SF  +ELP++T  + NP HLLD+ RF SD+V +F+R Q E++R HAP   V HN
Sbjct: 183 WSMEYPSFDSIELPNVTPTDANPIHLLDFRRFMSDEVTSFHREQAEVVRRHAPHADVLHN 242

Query: 242 FMGFFTDLDAFALAQD--LDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAFHHDL 299
           FMGFFT  D +  A +  +D A+WDSYP+  T+++ L   +K RYARTGHPDV+AF HD 
Sbjct: 243 FMGFFTTFDHYRFASNGSIDVATWDSYPIARTEVIALAETDKARYARTGHPDVSAFDHDR 302

Query: 300 YRGVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQ 359
           YRG+G+GRFWVMEQ+ GPVNWAP NP PAPGMVRLW +EA AHGAE+VSYFRWRQAPFAQ
Sbjct: 303 YRGIGQGRFWVMEQEAGPVNWAPWNPVPAPGMVRLWAYEAFAHGAELVSYFRWRQAPFAQ 362

Query: 360 EQMHAGLHRPDSAPDQGFFEAKRVAEELA------ALALP-PVAQAPVALVFDYEAAWIY 412
           EQMH+GLH PD+ P  G  E  R A+E+A      ALA   P  +APVALVFDYE  W++
Sbjct: 363 EQMHSGLHLPDNTPSPGGREVARAAQEIAKSAELSALAQSGPAGRAPVALVFDYETQWMF 422

Query: 413 EVQPQGAEWSYLGLVYLFYSALRRLGLDVDVVPPGASLRGYAFAVVPSLPIVREEALEAF 472
           E+Q    ++ Y  L + +Y  LR + LDVD+V   A L GYA  VVP L ++    ++  
Sbjct: 423 EIQRHAKDFDYQTLAFEYYRTLREMSLDVDIVSAHADLDGYALIVVPGLAVLPPGFVDTI 482

Query: 473 REAEGPVLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLL-EVAEGALGR 531
           R +    + GPR+GSKT  F IP ELPPGPLQ LLP KV+ V+SL P L      G +  
Sbjct: 483 RRSSAQWVIGPRTGSKTLDFAIPSELPPGPLQTLLPFKVLEVDSLRPSLQPSTTLGGVSG 542

Query: 532 FPLGLWREWVEA--PLKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAAEAGL 589
             L  WRE +E    ++ L  F DG  A+    R  Y +AW  P L   LL A A +A L
Sbjct: 543 IALH-WREHLETRDGVEVLARFDDGWPAVVARDRVRYASAWFDPPLHRALLEAAARDASL 601

Query: 590 KVLSLPEGLRLRRRGTWVFAFNYGPEAVEAPASEGARFLLGSRRVGPYDLAVWEEA 645
             + LPEG+R+RRRG   FAFN+G +AVEAPA   ARF+LGSR +G  D+ VW +A
Sbjct: 602 NPVHLPEGVRIRRRGPLTFAFNFGAQAVEAPAPANARFVLGSRTLGTADVCVWTQA 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: 1484
Number of extensions: 87
Number of successful extensions: 5
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: 657
Length adjustment: 38
Effective length of query: 607
Effective length of database: 619
Effective search space:   375733
Effective search space used:   375733
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 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