GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N2E3

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AO353_04290 AO353_04290 1-pyrroline dehydrogenase

Query= BRENDA::V4GH04
         (496 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04290
          Length = 474

 Score =  358 bits (918), Expect = e-103
 Identities = 202/481 (41%), Positives = 284/481 (59%), Gaps = 10/481 (2%)

Query: 16  QMLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPP 75
           ++LI GQ V+ + G    V+NPA G +L E+ +     V+AAV +A A      W + PP
Sbjct: 4   KLLINGQLVTGE-GPAQAVFNPALGRVLVEINEASEAQVDAAVRAADAAFEG--WSQTPP 60

Query: 76  SARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTG 135
             R  +LL+LAD+++ HG+ELA+LE+ N GK    +   E+ A A   R+ AG +  ++G
Sbjct: 61  KDRSLLLLKLADVIQAHGEELAKLESDNCGKPYSAALNDEIPAIADVFRFFAGASRCMSG 120

Query: 136 STLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAE 195
           S     LP        +  +R PVGV+A+I PWN+PL+M  WKIAPALA GNTVVLKP+E
Sbjct: 121 SAGGEYLP-----GHTSMIRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSE 175

Query: 196 ETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGS 255
           +TPLTALRLAELA E   PAG LN+V GRG T G  LV HPKV  V+ TGS   G  I S
Sbjct: 176 QTPLTALRLAELASEI-FPAGVLNLVFGRGPTVGSPLVTHPKVRMVSLTGSIATGSNIIS 234

Query: 256 ACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYE 315
           +   S+K + +ELGGK+PVI+  D D   A EG     F+N GQ CTA  R+Y    IYE
Sbjct: 235 STADSVKRMHMELGGKAPVIIFDDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQAGIYE 294

Query: 316 DVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPC 375
             +++L     SI  G   +    +GP+++ +H + V   +   I      +  G +A  
Sbjct: 295 KFVEKLGAAVSSIKYGLQDDPSTELGPLITAQHRDRVAGFVERAIAQPHIRLITGGKAVE 354

Query: 376 AQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTN 435
             GFF +PT+ A+  ++D  ++ +EVFGPV+  T F+D  +V+  AN S YGL +S+WT+
Sbjct: 355 GNGFFFEPTVLAD-ARQDDEIVRREVFGPVVSVTSFADETQVLAWANDSDYGLASSVWTS 413

Query: 436 DLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSLVIA 495
           D+  A R+   L+ G  WVNTH M+   +P GG K SG G++     +E YTT R ++  
Sbjct: 414 DVGRAHRLAARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTTVRHVMFK 473

Query: 496 Y 496
           +
Sbjct: 474 H 474


Lambda     K      H
   0.317    0.134    0.395 

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: 603
Number of extensions: 21
Number of successful extensions: 5
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: 496
Length of database: 474
Length adjustment: 34
Effective length of query: 462
Effective length of database: 440
Effective search space:   203280
Effective search space used:   203280
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 (21.7 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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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