GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4408 2-Keto-D-gluconate
           dehydrogenase (EC 1.1.99.4), membrane-bound, cytochrome
           c
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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