GapMind for catabolism of small carbon sources

 

Alignments for a candidate for catB in Burkholderia phytofirmans PsJN

Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate BPHYT_RS10675 BPHYT_RS10675 muconate cycloisomerase

Query= metacyc::MONOMER-14643
         (382 letters)



>FitnessBrowser__BFirm:BPHYT_RS10675
          Length = 385

 Score =  429 bits (1104), Expect = e-125
 Identities = 218/375 (58%), Positives = 280/375 (74%), Gaps = 2/375 (0%)

Query: 1   MLATA--IESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLA 58
           M+AT   IES++TI+VD+PTIRPH+L++ TM  QTLV++R+RCADG+ G+GE TTIGGLA
Sbjct: 1   MIATPVKIESVDTILVDVPTIRPHRLSVATMNCQTLVLVRIRCADGLIGVGEGTTIGGLA 60

Query: 59  YGNESPDSIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGK 118
           YG ESP+SIK NID +FAPLL G D+    AAM +L    +GN FAKS +ETAL DA  +
Sbjct: 61  YGEESPESIKVNIDTYFAPLLKGMDATRPGAAMAKLRELFQGNRFAKSALETALFDAQAQ 120

Query: 119 RLGLPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRD 178
           RLG+P+SEL GGRVRD++ VAWTLASGDT++DI EAE++ + +RHR+FKLKIG   V  D
Sbjct: 121 RLGVPLSELFGGRVRDSVEVAWTLASGDTQRDIDEAEQVYEAKRHRVFKLKIGTRAVADD 180

Query: 179 LAHVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARL 238
           +AHV+AI+KA+  R  VRVDVNQAW E+ A+ A R     G+ L+EQPI+  NR G+ RL
Sbjct: 181 VAHVVAIQKAVQGRGEVRVDVNQAWSESDAIWAARRFADAGVTLIEQPIAAENRAGLKRL 240

Query: 239 NAMSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALY 298
             ++  PIMADE++    DAF +A   AA VFA+KIA++GG       A+IA AA I LY
Sbjct: 241 TDLALVPIMADEALHGPADAFVVASARAADVFAVKIAQSGGLVGAAHVAAIASAANIDLY 300

Query: 299 GGTMLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGL 358
           GGTMLEG +GT+ASA  F T  +L W TELFGPLLLTE+IL+EPL Y +F LH+P  PGL
Sbjct: 301 GGTMLEGAVGTIASAQLFSTFGELKWGTELFGPLLLTEEILTEPLRYENFALHLPEGPGL 360

Query: 359 GLSLDEERLAFFRRD 373
           G++LD +++   RRD
Sbjct: 361 GVTLDWDKIDRLRRD 375


Lambda     K      H
   0.319    0.136    0.386 

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: 399
Number of extensions: 8
Number of successful extensions: 1
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: 382
Length of database: 385
Length adjustment: 30
Effective length of query: 352
Effective length of database: 355
Effective search space:   124960
Effective search space used:   124960
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: 50 (23.9 bits)

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

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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:

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:

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:

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:

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