GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Pseudomonas fluorescens FW300-N2E2

Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate Pf6N2E2_4408 2-Keto-D-gluconate dehydrogenase (EC 1.1.99.4), membrane-bound, cytochrome c

Query= SwissProt::O34215
         (441 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4408
          Length = 474

 Score =  262 bits (669), Expect = 2e-74
 Identities = 169/443 (38%), Positives = 228/443 (51%), Gaps = 51/443 (11%)

Query: 2   MKSILALVLGTLSFAALADDQANDALVKRGEYLARAGDCVACHSVKGGQPFAGGLPMATP 61
           M+++LA  L  ++ +     +  D     G+ LA A DCVACHS  GG+PFAGG P+ +P
Sbjct: 19  MRNMLAGGLALMTISLATHGETLDTSASPGKRLAVAADCVACHSTVGGKPFAGGYPLNSP 78

Query: 62  IGTIYSTNITPDKTTGIGDYSYDDFQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKAL 121
           +GTIYSTNITP ++ GIG Y+  DF +AVR GV  +G  LYPAMPY SYA ++D D+ AL
Sbjct: 79  MGTIYSTNITPSRSAGIGQYTQADFARAVRDGVTPDGTHLYPAMPYTSYAKMTDSDVAAL 138

Query: 122 YAYFMHGVAPVAQANKDSDIPWPLSMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYL 181
           Y YFM  V PV   +  +++ +P ++R  +  W  +F    K F+    +   + RG YL
Sbjct: 139 YQYFMDEVEPVDTPSPKTELDFPFNIRASMLGWNALFHRQ-KRFEADPGKSAQVNRGDYL 197

Query: 182 VEGLGHCGACHTPRSITMQEKALSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSE 241
           V  L HC  CHTPR++ M   A  N  A   LSG S  +  W A N+  D   G+G WS 
Sbjct: 198 VNALAHCDTCHTPRNVLM---AADNAKA---LSGGS--LGAWYAPNITSDKTSGIGAWSS 249

Query: 242 DDLRQFLRYGRNDHTA-AFGGMTDVVEHSLQHLSDDDITAIARYLK-----SLGAKDASQ 295
           D+L  +LR G  +  A A G M + VEHSLQ+L ++D+ AIA YL      + G + A  
Sbjct: 250 DELVAYLRSGHVEGKAQAAGPMAEAVEHSLQYLGEEDLKAIAAYLLQTQPIATGERQARH 309

Query: 296 TVFTQDDQVAKALWKGDDSQTGASVYVDSCAACHKTDGSRLSALLPGAAWQPGGAGEPDP 355
           T     +              G  ++  +CA CH                Q  G G  + 
Sbjct: 310 TFGQASNDELNLRGGKPQDNPGWHIFSGTCANCH----------------QANGEGTREY 353

Query: 356 TSLIHIVLTG-----------GTLPGVQGAPTAITMPAFG------WRLNDQQVADVVNF 398
            SL H   T            G    V G   AI MPAFG       RL+DQQ+ADV N+
Sbjct: 354 PSLFHNTATSRRDNLIATIVYGVHREVDG--VAIDMPAFGPGALFTDRLDDQQIADVSNY 411

Query: 399 IRGSWGNGAKATVTAKDVASLRK 421
           +   +GN A   VTA DVA +R+
Sbjct: 412 VLSRYGN-AGLNVTAADVAQVRE 433


Lambda     K      H
   0.317    0.133    0.409 

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: 612
Number of extensions: 44
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: 441
Length of database: 474
Length adjustment: 33
Effective length of query: 408
Effective length of database: 441
Effective search space:   179928
Effective search space used:   179928
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: 41 (21.6 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