GapMind for catabolism of small carbon sources

 

Alignments for a candidate for antA in Burkholderia phytofirmans PsJN

Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate BPHYT_RS07855 BPHYT_RS07855 benzoate 1,2-dioxygenase subunit alpha

Query= SwissProt::O85673
         (471 letters)



>FitnessBrowser__BFirm:BPHYT_RS07855
          Length = 452

 Score =  404 bits (1039), Expect = e-117
 Identities = 210/435 (48%), Positives = 291/435 (66%), Gaps = 17/435 (3%)

Query: 23  DGVYRIARDMFTEPELFELEMELIFEKVWIYACHESEIPNNNDFVTVQIGRQPMIVSRDG 82
           +GV+R  RD+FT  ELFELEM+ IFE  W+Y  HES+IPNNND+ T  IGRQP++V+RD 
Sbjct: 25  NGVFRCRRDIFTNAELFELEMKHIFESNWVYLAHESQIPNNNDYYTTWIGRQPVVVTRDK 84

Query: 83  KGELHAMVNACEHRGATLTRVAKGNQSVFTCPFHAWCYKSDGRLVKVK--APGEYCEDFD 140
            GELHA++NAC H+GA L R   GN+  FTCPFH W + + G+L+KVK     EY   F+
Sbjct: 85  SGELHAVINACAHKGAMLCRKKHGNKGTFTCPFHGWSFANTGKLLKVKDVKTTEYPIQFN 144

Query: 141 KS-SRGLKQ-GRIASYRGFVFVSLDTQATDSLEDFLGDAKVFLDLMVDQSPTGELEVLQG 198
            + S  LK+  R  SYRGF+F +L+  A   LED+LG+ +V +D +VDQ+P G LEVL+G
Sbjct: 145 TNGSHDLKKVARFQSYRGFLFGTLNADAIP-LEDYLGETRVIIDQIVDQAPDG-LEVLRG 202

Query: 199 KSAYTFAGNWKLQNENGLDGYHVSTVHYNYVSTVQHRQQVNAAKGDELDTLDYSKLGAGD 258
            S+Y + GNWK+Q ENG DGYHVSTVH+NY +T+  R++V   K   +D   +SK  AG 
Sbjct: 203 NSSYIYDGNWKVQMENGCDGYHVSTVHWNYAATMD-RRKVEGTKA--VDANSWSKSVAGV 259

Query: 259 SETDDGWFSFKNGHSVLFSDMPNPTVRPGYNTVMPYLVEKFGEKRAEWAMHRLRNLNLYP 318
                  + F++GH +L++   NP VRP Y      +  + GE +A++ +++ RNL LYP
Sbjct: 260 -------YGFEHGHILLWTKTMNPEVRPVYQ-YRDEIKARVGEVKADFIVNQTRNLCLYP 311

Query: 319 SLFFMDQISSQLRIIRPVAWNKTEVISQCIGVKGESSEARRNRIRQFEDFFNVSGLGTPD 378
           ++F MDQ S+Q+R++RP++ +KTEV   C   KGES+  R  RIRQ+EDFFNVSG+GT D
Sbjct: 312 NVFLMDQFSTQIRVVRPISVDKTEVSIFCFAPKGESASDRATRIRQYEDFFNVSGMGTAD 371

Query: 379 DLVEFREQQKGFQGRIERWSDISRGYHQWTYGPTQNSQDLGIEPVITGREFTHEGLYVNQ 438
           DL EFR  Q G+ G    W+D+SRG   W  G   N++++G++PVI+G     EGL+V Q
Sbjct: 372 DLEEFRACQAGYAGTTAMWNDLSRGAPLWVEGADANAKNMGLKPVISGERSEDEGLFVCQ 431

Query: 439 HGQWQRLILDGLNKK 453
           H  W  ++ D L K+
Sbjct: 432 HEYWVHVMRDALRKE 446


Lambda     K      H
   0.319    0.136    0.420 

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: 600
Number of extensions: 23
Number of successful extensions: 6
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: 471
Length of database: 452
Length adjustment: 33
Effective length of query: 438
Effective length of database: 419
Effective search space:   183522
Effective search space used:   183522
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 (21.8 bits)
S2: 51 (24.3 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