Alignments for a candidate for lacZ in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Pseudomonas stutzeri RCH2

Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate GFF1538 Psest_1575 Beta-glucosidase-related glycosidases

Query= SwissProt::E7CY69
         (757 letters)



>FitnessBrowser__psRCH2:GFF1538
          Length = 763

 Score =  241 bits (615), Expect = 1e-67
 Identities = 209/685 (30%), Positives = 313/685 (45%), Gaps = 83/685 (12%)

Query: 36  GIPSYMITDGPHGLRKSLASSAGETDLDDSVPATCFPPAAGLSSSWNPELIHKVGEAMAE 95
           GIP +   D  HG R                  T FP +  L+SSW+ E I   G   A 
Sbjct: 98  GIPIFFAYDVIHGHR------------------TIFPISLALASSWDLEAIALSGRVSAI 139

Query: 96  ECIQEKVAVILGPGVNIKRNPLGGRCFEYWSEDPYLAGHEAIGIVEGVQSK------GVG 149
           E   + + +   P V+I R+P  GR  E + EDPYL    A  +V   Q +       V 
Sbjct: 140 EASADGLDLTFAPMVDITRDPRWGRTSEGFGEDPYLVSQIAGTLVRAYQGERLSAADSVM 199

Query: 150 TSLKHFAANNQ-ETDRLRVDARISPRALREIYFPAFEHIVKKAQPWTIMCSYNRINGVHS 208
            S+KHFA     E  R      +SP+ + + Y P +   V  A    +M + N +NG+ +
Sbjct: 200 ASVKHFALYGAVEGGRDYNVVDMSPQRMHQDYLPPYRAAVD-AGAGGVMVALNTVNGMPA 258

Query: 209 AQNHWLLTDVLRDEWGFDGIVMSDWGA-----------DHDRGA--SLNAGLNLEMPPSY 255
           + N WLL D+LRD+WGF G+ +SD GA           D    A  ++ AG++L M  S 
Sbjct: 259 SANRWLLRDLLRDDWGFRGLNISDHGAIDELLRHGVARDGREAARLAIEAGIDLSMHDSL 318

Query: 256 TDDQIVYAVRDGLITPAQLDRMAQGMIDLVNKTRAAMSIDNYR---------FDVDA--- 303
              ++   V  G + P +L   A G + L  K    +  D YR          +V+A   
Sbjct: 319 YLQELPGLVERGEV-PIELIDQAVGRV-LGAKYDLGLFHDPYRRIGQAADDPVEVNAESR 376

Query: 304 -HDEVAHQAAIESIVMLKNDDAILPLN-------AGPVA----------NPSATPQKIAV 345
            H + A + A +S+V+L+N +  LPL         GP+A          + +    +   
Sbjct: 377 LHRQAARRVARDSLVLLENPEQTLPLRKDATIALVGPLADSHVDMLGSWSAAGVAAQTVT 436

Query: 346 IGEFARTPRYQGGGSSHITPTKMTSFLDTLAERGIKADFAPGFTLDLEPADP-ALESEAV 404
           + +       +GG   H     +T     +          P  +LD  P  P A+  EAV
Sbjct: 437 LRQGLEAAVGKGGQIIHARGASVTDDAGMIKYLNFLNWDRPEVSLD--PRTPQAMIDEAV 494

Query: 405 ETAKNADVVLMFLGLPEAVESEGFDRDTLDMPAKQIALLEQVAAANQNVVVVLSNGSVIT 464
             A+ ADV++  +G    +  E   R +L +PA Q ALLE + A  + +VVVL NG  + 
Sbjct: 495 RAAREADVIVAAVGEARGMSHESSSRTSLALPASQQALLEALVATGKPLVVVLMNGRPLQ 554

Query: 465 VAPWAKNAKGILESWLLGQSGGPALADVIFGQVSPSGKLAQSIPLDINDDPSMLNWPGEE 524
           +    ++A  +LE+W  G  GG A+ADV+FG  +PSGKL  S P  +   P+  N P   
Sbjct: 555 LGWVKEHADAVLETWFAGTEGGHAIADVLFGAHNPSGKLPISFPRSVGQIPTYYNHP-RL 613

Query: 525 GHVDYGEGVFAGY--RYYDTYGKAVDYPFGYGLSYATFEITGVAVAKTGANTA---TVTA 579
           G   Y EG    Y  +Y++    A+ YPFGYGLSY  FE++   +++   N      V+ 
Sbjct: 614 GR-PYVEGRPGNYTSQYFEEPNGAL-YPFGYGLSYTDFELSKPQLSRRTLNRGQKLEVSV 671

Query: 580 TVTNTSDVDAAETVQVYVVPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDERAFAYW 639
           TV NT     A  VQ+Y+        RP  ELKGFTK  L+ GE++ V   L E    ++
Sbjct: 672 TVKNTGARAGATVVQLYLQDLVGSSVRPVKELKGFTKLMLEPGETQLVRFVLGEEDLKFY 731

Query: 640 SEKYNDWHVEAGEYAIEVGVSSRDI 664
             +  D   E GE+ +++G+ S+ +
Sbjct: 732 DARL-DHVAEPGEFEVQLGLDSQSV 755


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: 1288
Number of extensions: 60
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 757
Length of database: 763
Length adjustment: 40
Effective length of query: 717
Effective length of database: 723
Effective search space:   518391
Effective search space used:   518391
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