GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB 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)



>FitnessBrowser__pseudo3_N2E3:AO353_29295
          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 (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