GapMind for catabolism of small carbon sources

 

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

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate Pf1N1B4_5582 Quinate/shikimate dehydrogenase [Pyrroloquinoline-quinone] (EC 1.1.99.25)

Query= BRENDA::Q70JN9
         (743 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5582
          Length = 807

 Score =  481 bits (1239), Expect = e-140
 Identities = 268/697 (38%), Positives = 375/697 (53%), Gaps = 52/697 (7%)

Query: 65  GPSPYAPQAPGVNAANLPDIGSMDPNDVPQMAPQQSASPASGDWAAYGHDDSQMRYSPLS 124
           G   + P AP     + P + ++DP            + A  +W  YG+D+   R++ L 
Sbjct: 140 GAGMFVPHAPVSPTGDGPGLTTVDP------------AKAQKNWEHYGNDEGGSRFAALD 187

Query: 125 EITPQNADQLKVAFVYHTGSYPRPGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATG 184
           +I   N  +L  A+ Y+TG        N    + TP++VGD +++C+  N+++ +D  TG
Sbjct: 188 QINRSNVSKLVPAWTYNTGDIAI-SDGNGAEDQMTPLQVGDKVFICTPHNNLIALDADTG 246

Query: 185 KEIWRHNINEKYEAIPYTAACKGVTYFTSS----------------QVPEGQPCHNRILE 228
           K++W++ IN K         C+GV YF ++                 +P G  C  R+L 
Sbjct: 247 KQLWKNEINAKTRV---WQRCRGVAYFDATAALAQPADGSTPVKPVSIPAGANCQRRLLT 303

Query: 229 GTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEV 288
            T+D RLIAVDA TG  C+GFGN GQV+L  GLG+    +  +++ P +    VVV   V
Sbjct: 304 NTIDARLIAVDADTGEFCQGFGNNGQVDLKAGLGDVPDSYYQLSSAPLMAGTTVVVGGRV 363

Query: 289 LDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNA 348
            D  +   P GVIRG+D  +G+  WA+D   P D   P   + Y R TPNSWA M+ D A
Sbjct: 364 ADNVQTDMPGGVIRGFDVVTGEMRWAFDPGNPEDKQAPAAGSTYVRSTPNSWAPMSYDPA 423

Query: 349 LGLVYVPTGNSASDYYSALRSPEENKVSSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQ 408
           +  V++P G+S++D Y   R+   +K  ++V+AL+  TG  +WV+QTVH D+WD+D+  Q
Sbjct: 424 MNTVFLPMGSSSTDIYGVERTALNHKYGASVLALNATTGEEKWVYQTVHNDLWDFDLPMQ 483

Query: 409 ATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQ 468
            +L+D    DG  VPA+++ TK GQ FVLDR  GKP+  VEE P  +   IP +P S TQ
Sbjct: 484 PSLIDFTKADGSKVPAVVIGTKAGQIFVLDRATGKPLTKVEEVPVKTSN-IPNEPYSLTQ 542

Query: 469 PWSTGMPALRVPDLKETDMWGMSPIDQLFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNG 528
           P S GMP +    L E+DMWG +P DQL CRI F++  Y G +T P  D   + +PG  G
Sbjct: 543 PKSVGMPEIGAQTLTESDMWGATPFDQLLCRISFKKMRYDGLYTAPGTDIS-LSFPGSLG 601

Query: 529 GSDWGSVSYDPQSGILIANWNITPMYDQLVTRKKADELGLMPIDDPNYKPGGGGAE-GNG 587
           G +WG +S DP  G +  N     ++ Q++  KK          D     GG     G G
Sbjct: 602 GMNWGGISTDPVHGFIFVNDMRLGLWIQMIAAKK----------DAKASSGGEALNTGMG 651

Query: 588 A--MDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAIDMKHGQKVLWQHPLGTARANGPWG 645
           A  + GTPY +    F     G+ C  PP+G +TAIDMK  QKV WQ P+GT +  GP G
Sbjct: 652 AVPLKGTPYAVNKNRFL-SVAGIPCQAPPFGTLTAIDMK-TQKVAWQVPVGTVQDTGPLG 709

Query: 646 LPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIRAIDEHTGKVVWSAVLPGGGQANPM 705
           +   LP  IG P  GG++ T GG+VFIA   D  +RA +   GK  W A LP G Q  PM
Sbjct: 710 IKMHLPLPIGMPTLGGTLSTQGGLVFIAGTQDYYLRAFNSANGKEAWKARLPVGSQGGPM 769

Query: 706 TYEA--NGHQYVAIMAGGHHFMMTPVSDQLVVYALPD 740
           TY +   G QYV I AGG         D ++ YALPD
Sbjct: 770 TYVSPKTGKQYVVITAGGAR-QSPDRGDYVIAYALPD 805


Lambda     K      H
   0.315    0.134    0.428 

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: 1988
Number of extensions: 121
Number of successful extensions: 8
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: 743
Length of database: 807
Length adjustment: 41
Effective length of query: 702
Effective length of database: 766
Effective search space:   537732
Effective search space used:   537732
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: 42 (22.0 bits)
S2: 55 (25.8 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