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

GapMind for catabolism of small carbon sources

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

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Pf6N2E2_1370 Putative benzaldehyde dehydrogenase oxidoreductase protein (EC 1.2.1.28)

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1370
          Length = 490

 Score =  208 bits (529), Expect = 4e-58
 Identities = 157/489 (32%), Positives = 243/489 (49%), Gaps = 36/489 (7%)

Query: 6   NGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVV 65
           NGDW+   G  +    P +GE L +   AD+A + +A R A  A P WA L   +R A+ 
Sbjct: 20  NGDWVPASGPLQSIIEPATGERLMRCATADSADIAKASRDAALAQPGWAALGPRQRAAIF 79

Query: 66  ERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPD 125
            + A + E +  EL   +ARETG   ++   EV      I +  +A  + +      +P 
Sbjct: 80  RKAAEVAEHSFNELALYVARETGAALFKGQHEVR---EAIVLLHQAAGLLSQAHGVVLPS 136

Query: 126 GAASL---RHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGE-AVM 181
            A  L   R +PHGV+ V  P+NFP  L    + PAL AGN ++ KP   TP SG   + 
Sbjct: 137 EAGRLSYARRQPHGVVGVISPFNFPLVLSMRSVAPALAAGNAVVLKPDPQTPVSGGFLIA 196

Query: 182 RLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILA 241
           RL++ AGLP G+L ++ G  + G+AL    ++  + FTGS   G ++  +++G+  K +A
Sbjct: 197 RLFEVAGLPKGLLQVLPGAADAGEALCRDPNVRMIAFTGSTGAGRKV-AEVAGRNLKKVA 255

Query: 242 LEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAV 301
           LE+GG NPLII E AD+D A       A++  GQ C  A  L+L   +  +    +LV  
Sbjct: 256 LELGGKNPLIILEDADLDLAARNAAWGAWLHQGQIC-MATGLILAHESIAEELTRKLVEK 314

Query: 302 SQRLTPGNWDDEPQPFIGGLISEQAAQQV-------VTAWQQLEAMGGRPLLAPRLLQAG 354
           ++ LT GN   + +  +G LI+++  ++V       V A  +LEA G       RL    
Sbjct: 315 ARALTVGN-AAQGEAALGPLINQRQLKRVHDIVSDSVRAGARLEAGGEH----DRLFYQA 369

Query: 355 TSL--LTPGIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPER 412
           T L  + PG+          DEE+FGP+  V  + T DEA+ +AN T +GL+  ++S   
Sbjct: 370 TVLSGVKPGMRAF-------DEEIFGPVATVVSFATDDEAVELANRTEYGLAAAIISSSV 422

Query: 413 EKFDQLLLEARAGIVNWNKPLTGAASTAPFGGIGASGN----HRPSAWYAADYCAWPMAS 468
            +   +    + G+++ N          PFGG GASGN      P+ W   +Y  W   +
Sbjct: 423 GRAMAIGERLQCGMLHINDQTVADECINPFGGRGASGNGGSVGGPADW--DEYTQWQWVT 480

Query: 469 LESDSLTLP 477
           ++  +   P
Sbjct: 481 VKDKAPVYP 489


Lambda     K      H
   0.318    0.134    0.412 

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: 629
Number of extensions: 36
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: 492
Length of database: 490
Length adjustment: 34
Effective length of query: 458
Effective length of database: 456
Effective search space:   208848
Effective search space used:   208848
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: 52 (24.6 bits)

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

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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, 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

GapMind for catabolism of small carbon sources