GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Pseudomonas fluorescens FW300-N2E3

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate AO353_29295 AO353_29295 aldehyde dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_29295 AO353_29295 aldehyde
           dehydrogenase
          Length = 496

 Score =  777 bits (2006), Expect = 0.0
 Identities = 380/494 (76%), Positives = 433/494 (87%)

Query: 4   LTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAV 63
           +TR+ WEQ  Q L IEGRAFI+G Y  A+S +TFEC+SPVDGRFLA VAS D ADAN AV
Sbjct: 3   ITRSGWEQHFQSLTIEGRAFIDGHYCSALSRDTFECVSPVDGRFLANVASTDEADANAAV 62

Query: 64  ENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPG 123
           + AR  F+SGVW++LAPA+RK  LIRFADL+  N EELALLETLDMGKPI DS +IDIP 
Sbjct: 63  QVARRAFDSGVWAKLAPAERKRILIRFADLILANQEELALLETLDMGKPISDSMAIDIPA 122

Query: 124 AAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALA 183
            A AI W+AEAIDK+YDEVA TPHDQLGLVTREP GVV AIVPWNFPL+MA WK  PALA
Sbjct: 123 TANAIRWSAEAIDKIYDEVAATPHDQLGLVTREPSGVVAAIVPWNFPLIMASWKFAPALA 182

Query: 184 TGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFT 243
            GNS +LKPSEKSPLTAIRIAQLA++AGIP GV NVLPG+GHTVGKALALHMDVD L FT
Sbjct: 183 AGNSFILKPSEKSPLTAIRIAQLALDAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAFT 242

Query: 244 GSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCT 303
           GST IAKQL++YAG+SNMKR+WLEAGGKSPN+VFADAPDL+AAA AAASAIAFNQGEVCT
Sbjct: 243 GSTAIAKQLLIYAGQSNMKRVWLEAGGKSPNVVFADAPDLRAAATAAASAIAFNQGEVCT 302

Query: 304 AGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKD 363
           AGSRLLVERSI+++F+P++VEAL+ WKPG+ LDP+TTVGA+VD +Q++ VL YI  G + 
Sbjct: 303 AGSRLLVERSIREQFIPLLVEALQAWKPGHALDPETTVGAVVDQRQLDNVLRYISIGKEQ 362

Query: 364 GAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIAN 423
           GA+L+AGG R LE+TGG YVEP IFDGVTNAM IA+EEIFGPVLS+I FDTAEEA+AIAN
Sbjct: 363 GAQLIAGGNRALEDTGGLYVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALAIAN 422

Query: 424 DTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHA 483
           D+ +GLAAG+WTS++SKAH  AR +RAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHA
Sbjct: 423 DSIFGLAAGVWTSNLSKAHTFARGLRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHA 482

Query: 484 LEKYTELKATWIKL 497
            +KYTELKATWIKL
Sbjct: 483 FDKYTELKATWIKL 496


Lambda     K      H
   0.316    0.132    0.390 

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: 757
Number of extensions: 18
Number of successful extensions: 2
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: 497
Length of database: 496
Length adjustment: 34
Effective length of query: 463
Effective length of database: 462
Effective search space:   213906
Effective search space used:   213906
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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