Alignments for a candidate for lacZ in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Pedobacter sp. GW460-11-11-14-LB5

Align Beta-galactosidase BoGH2A; Beta-gal; Glycosyl hydrolase family protein 2A; BoGH2A; EC 3.2.1.23 (characterized)
to candidate CA265_RS08540 CA265_RS08540 glycoside hydrolase family 2

Query= SwissProt::A7LXS9
         (851 letters)



>FitnessBrowser__Pedo557:CA265_RS08540
          Length = 802

 Score =  803 bits (2073), Expect = 0.0
 Identities = 399/830 (48%), Positives = 538/830 (64%), Gaps = 52/830 (6%)

Query: 36  SSLVSPRERSDFNADWRFHLGDGLQAAQPGFADNDWRVLDLPHDWAIEGDFSQENPSGTG 95
           +++ + R R  FN DW+F LGD   A  P + D  WR L LPHDW+IEG F ++NP+   
Sbjct: 2   TTVSTSRTRISFNKDWKFFLGDEPNAKSPAYNDIKWRKLTLPHDWSIEGKFDEKNPAKPE 61

Query: 96  GGALPGGVGWYRKTFSVDKADAGKIFRIEFDGVYMNSEVFINGVSLGVRPYGYISFSYDL 155
           GG LP G+GWYRK F        +I  IEFDGVY NSEV+ING  LG RPYGY SFSY++
Sbjct: 62  GGGLPTGIGWYRKEFIAPANFKNRIINIEFDGVYKNSEVWINGHYLGKRPYGYSSFSYEI 121

Query: 156 TPYLKWDEPNVLAVRVDNAEQPNSRWYSGCGIYRNVWLSKTGPIHVGGWGTYVTTSSVD- 214
           + +LK  + N +AV+VDN+ QP+SRWYSG GIYRNVWL+    + V   G +V T+ +  
Sbjct: 122 SKFLKPGK-NSIAVKVDNSAQPDSRWYSGSGIYRNVWLTSAAAVSVKRNGVFVKTTIISG 180

Query: 215 --------------EKQAVLNLATTLVNESDTNENVTVCSSLQDAEGREVAETRSSGEAE 260
                         E  A + +   L N+ +T     + +++ D +G ++ + +     +
Sbjct: 181 DKGQSVENRILSPGESMASIAVDIELENKFNTKGTYKILTTIFDDKGTKLQQKQWPMAVD 240

Query: 261 AGKEVVFTQQLTVKQPQLWDIDTPYLYTLVTKVMRNE-ECMDRYTTPVGIRTFSLDARKG 319
                + T  L++  P+LW ++ P +Y L+T++M+ + + +D YTT  GIR F+ DA+KG
Sbjct: 241 QNALKLVTNGLSIANPKLWSVEQPVMYKLLTEIMQADGKIIDSYTTAFGIRDFNFDAQKG 300

Query: 320 FTLNGRQTKINGVCMHHDLGCLGAAVNTRAIERHLQILKEMGCNGIRCSHNPPAPELLDL 379
           F+LNG+  KI GVC+HHDLG LGAAVN RA+ER L+I+K MG N IR +HNPPAPE LDL
Sbjct: 301 FSLNGKPMKILGVCLHHDLGALGAAVNVRAMERQLEIMKAMGVNAIRTAHNPPAPEFLDL 360

Query: 380 CDRMGFIVMDEAFDMWRKKKTAHDYARYFNEWHERDLNDFILRDRNHPSVFMWSIGNEVL 439
           CD+MGF+VMDEAFDMW KKK  +DY   F EWH+ DL + I RDRNHPS+ +WSIGNE+ 
Sbjct: 361 CDKMGFLVMDEAFDMWVKKKNKNDYHLNFPEWHKSDLEEMIKRDRNHPSIILWSIGNEIR 420

Query: 440 EQWSDAKADTLSLEEANLILNFGHSSEMLAKEGEESVNSLLTKKLVSFVKGLDPTRPVTA 499
           EQ+                               +S    +TK+LV  VK LD TRPV +
Sbjct: 421 EQF-------------------------------DSTGVAITKELVGIVKNLDKTRPVIS 449

Query: 500 GCNEPNSG-NHLFRSGVLDVIGYNYHNKDIPNVPANFPDKPFIITESNSALMTRGYYRMP 558
              E  +  N ++++  LD+ G NY++K   + P N+P   F+ TE+ SAL TRG+Y   
Sbjct: 450 ALTETKAEKNFIYQANALDIYGLNYNHKLYKDFPENYPGVKFLATETTSALETRGFYDT- 508

Query: 559 SDRMFIWPKRWDKSFAD--STFACSSYENCHVPWGNTHEESLKLVRDNDFISGQYVWTGF 616
           +D +  WPK     F +  S ++ S+Y+N    WG+THEE+    +  D +SG +VWTGF
Sbjct: 509 ADTIRRWPKDGKTKFTEGNSEWSASAYDNVSAYWGSTHEETWAAAKKYDHVSGLFVWTGF 568

Query: 617 DYIGEPTPYGWPARSSYFGIVDLAGFPKDVYYLYQSEWTDKQVLHLFPHWNWTPGQEIDM 676
           DY+GEP PY WPARSSYFGIVDLAGFPKD YY+YQSEWT+K VLH+ PHWNW  G+ +++
Sbjct: 569 DYLGEPLPYPWPARSSYFGIVDLAGFPKDSYYMYQSEWTNKPVLHILPHWNWKQGKSVEV 628

Query: 677 WCYYNQADEVELFVNGKSQGVKRKDLDNLHVAWRVKFEPGTVKVIARESGKVVAEKEICT 736
           W YYN ADEVEL++NGKS G + K  D+LHV W+V FEPGT+K ++R++GK V  +E+ T
Sbjct: 629 WAYYNNADEVELYLNGKSLGKRSKQGDDLHVLWKVPFEPGTLKAVSRKNGKEVLVREMKT 688

Query: 737 AGKPAEIRLTPDRSILTADGKDLCFVTVEVLDEKGNLCPDADNLVNFTVQGNGFIAGVDN 796
           AG PA+I L  DR  + ADGKDL F+TV +LD  GN+ P+A+NLV+F V G GFIAGVDN
Sbjct: 689 AGDPAKIELIADRKNIKADGKDLSFITVRILDAAGNVVPNANNLVDFKVDGVGFIAGVDN 748

Query: 797 GNPVSMERFKDEKRKAFYGKCLVVIQNDGKPGKAKLTATSEGLRQAVLKI 846
           G   S+E FK   RKAF+G CL ++Q+  K G+ KLTA+S GL  + + I
Sbjct: 749 GFQASIEPFKANYRKAFHGLCLAILQSTEKSGEIKLTASSAGLASSSIII 798


Lambda     K      H
   0.319    0.136    0.431 

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: 1924
Number of extensions: 125
Number of successful extensions: 7
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: 851
Length of database: 802
Length adjustment: 42
Effective length of query: 809
Effective length of database: 760
Effective search space:   614840
Effective search space used:   614840
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 (21.7 bits)
S2: 56 (26.2 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