Alignments for a candidate for gdh in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Pseudomonas fluorescens FW300-N1B4

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate Pf1N1B4_5582 Quinate/shikimate dehydrogenase [Pyrroloquinoline-quinone] (EC 1.1.99.25)

Query= BRENDA::D4P700
         (796 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5582
          Length = 807

 Score =  603 bits (1555), Expect = e-176
 Identities = 341/819 (41%), Positives = 467/819 (57%), Gaps = 35/819 (4%)

Query: 1   MGKNSSSFSVVRF--LTVLFAVLT-GAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLW 57
           M K+  S SV R+    V F VL  G F   GG +LAT+GGSWY+++ G  ++++A LL+
Sbjct: 1   MTKSRPSASVSRWPIWVVAFGVLVFGLFFATGGGYLATLGGSWYFLLAGFGLIVSAVLLF 60

Query: 58  RRNSAALVVYALLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGK 117
           ++      ++A +++ T+ W + +VG +FW L  R   L +  +++ L  +Y  L +   
Sbjct: 61  KQRLQGAWLFAAVMVLTVIWALADVGLNFWPLISRLFALGVLSLFVAL--IYPHLRKANS 118

Query: 118 GALGAMGVALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQ 177
            A G  G AL    A+   +      V +  +  T D           A  +W  Y  D+
Sbjct: 119 LASGRSGYALSGVLAIAVVAGGAGMFVPHAPVSPTGDGPGLTTVDPAKAQKNWEHYGNDE 178

Query: 178 QGTRFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQI 237
            G+RF+ L QIN  NV +L  AW + TGD+   SD     D++TP+++ D +++CTPH  
Sbjct: 179 GGSRFAALDQINRSNVSKLVPAWTYNTGDIAI-SDGNGAEDQMTPLQVGDKVFICTPHNN 237

Query: 238 LFALDAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAA-----------KDASNTQP 286
           L ALDA TGKQ WK +   KT   +Q   CRGV+Y +  AA           K  S    
Sbjct: 238 LIALDADTGKQLWKNEINAKTR-VWQR--CRGVAYFDATAALAQPADGSTPVKPVSIPAG 294

Query: 287 ALCSRRIYLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITD 346
           A C RR+     D RL A+DA+TGE C  FGNNG++DL+          Y+ +S P++  
Sbjct: 295 ANCQRRLLTNTIDARLIAVDADTGEFCQGFGNNGQVDLKAGLGDVPDSYYQLSSAPLMAG 354

Query: 347 TTIVMAGAVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNS 406
           TT+V+ G V DN  T  P G IRGFDV TG++ W FDPG  +    PA   T+  ++PNS
Sbjct: 355 TTVVVGGRVADNVQTDMPGGVIRGFDVVTGEMRWAFDPGNPEDKQAPAAGSTYVRSTPNS 414

Query: 407 WAPAVYDPKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHD 466
           WAP  YDP ++ V+LPMG ++ DI+G  RT    +Y +SVLALNATTG+  W YQTVH+D
Sbjct: 415 WAPMSYDPAMNTVFLPMGSSSTDIYGVERTALNHKYGASVLALNATTGEEKWVYQTVHND 474

Query: 467 LWDMDLPSQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAK 526
           LWD DLP QP+L D T  DG+ VP +    K G IFVLDR TGK +    E PV      
Sbjct: 475 LWDFDLPMQPSLIDFTKADGSKVPAVVIGTKAGQIFVLDRATGKPLTKVEEVPVKTSNIP 534

Query: 527 GDHVSATQPYS-ELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTL 585
            +  S TQP S  +     Q LT+ DMWGAT +DQL+CR+ FK++RY+G +T P    +L
Sbjct: 535 NEPYSLTQPKSVGMPEIGAQTLTESDMWGATPFDQLLCRISFKKMRYDGLYTAPGTDISL 594

Query: 586 VFPGNLGMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETG 645
            FPG+LG   WGGIS DP       N M L    ++I       ++  K ++GG    TG
Sbjct: 595 SFPGSLGGMNWGGISTDPVHGFIFVNDMRLGLWIQMIA-----AKKDAKASSGGEALNTG 649

Query: 646 I--QPQYGVPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSP-- 701
           +   P  G PY V  N FLS  G+PC+ P +G ++A+D+KT +V W+  +GTV+D+ P  
Sbjct: 650 MGAVPLKGTPYAVNKNRFLSVAGIPCQAPPFGTLTAIDMKTQKVAWQVPVGTVQDTGPLG 709

Query: 702 --VPLPFKMGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPM 759
             + LP  +GMP LGG ++T G + FI  T D YLRAF++  G+  W+ARLP G Q  PM
Sbjct: 710 IKMHLPLPIGMPTLGGTLSTQGGLVFIAGTQDYYLRAFNSANGKEAWKARLPVGSQGGPM 769

Query: 760 TY--EVNGKQYVVIAAGGHGSFGTKLGDYVIAYALPDQK 796
           TY     GKQYVVI AGG      + GDYVIAYALPD +
Sbjct: 770 TYVSPKTGKQYVVITAGGARQSPDR-GDYVIAYALPDSQ 807


Lambda     K      H
   0.319    0.137    0.433 

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: 2205
Number of extensions: 144
Number of successful extensions: 17
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: 796
Length of database: 807
Length adjustment: 41
Effective length of query: 755
Effective length of database: 766
Effective search space:   578330
Effective search space used:   578330
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: 55 (25.8 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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