GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Pontimonas salivibrio CL-TW6

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_104913141.1 C3B54_RS02765 aldehyde dehydrogenase

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



>NCBI__GCF_002950575.1:WP_104913141.1
          Length = 507

 Score =  352 bits (903), Expect = e-101
 Identities = 200/476 (42%), Positives = 280/476 (58%), Gaps = 12/476 (2%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           +I G++T  V G  FE +SPV+G+   ++A     D + A++ A A   +  W + +  +
Sbjct: 23  WIGGQWTKPVKGNYFEDISPVNGKPFCEIARGTAEDIDAALDAAHAA--APAWGKASTTE 80

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R A L + AD++  NVE LA+ ET D GKPI ++ + DIP AA    +   A+     + 
Sbjct: 81  RAAVLNKIADVIDANVEMLAVAETWDNGKPIRETLNADIPLAADHFRYFVAAVRAQDGDF 140

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
                D       EP+GVVG I+PWNFP+LMA WKL PAL+ GN+VVLKP+E++P + + 
Sbjct: 141 QEMDGDTTAYHYHEPLGVVGQIIPWNFPILMAAWKLAPALSAGNAVVLKPAEQTPASILV 200

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           +A+L  +  +P GVLN++ G+G   GK LA    +  + FTG T   + ++ YA  +N+ 
Sbjct: 201 LAELIGDI-LPPGVLNIVNGFGAEAGKPLASSPRIRKIAFTGETTTGRLILQYAS-ANII 258

Query: 263 RIWLEAGGKSPNIVFADAP----DLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318
              LE GGKSPNI F D      D    A+      AFNQGEVCT  SR L+++S  D F
Sbjct: 259 PTTLELGGKSPNIFFDDVSQEKDDFYDKAQEGFVLFAFNQGEVCTCPSRALIQKSHYDSF 318

Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--- 375
           L   VE  K    GNPLD  T VGA     Q+  +LSYI+ G ++GA L+ GG R     
Sbjct: 319 LGDAVERTKKAIQGNPLDTDTQVGAQASNDQLEKILSYIDIGKQEGATLVCGGDRVDLGG 378

Query: 376 EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435
           +   G YVEP IF+G  N MR+ QEEIFGPV++V +FD  ++A+ IANDT YGL AG+W+
Sbjct: 379 DLADGYYVEPAIFEG-NNKMRLFQEEIFGPVVAVTSFDDYDDAIQIANDTLYGLGAGVWS 437

Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
            + + A++  R ++AG VWVN Y      A FGG+K SG GR+ +  AL  Y + K
Sbjct: 438 RNGNTAYRAGRDIQAGRVWVNNYHAYPAGAAFGGYKSSGIGRENNKLALSHYQQTK 493


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: 678
Number of extensions: 39
Number of successful extensions: 9
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: 507
Length adjustment: 34
Effective length of query: 463
Effective length of database: 473
Effective search space:   218999
Effective search space used:   218999
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 24 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