GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Williamsia sterculiae CPCC 203464

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_076482575.1 BW971_RS18685 aldehyde dehydrogenase family protein

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_900156495.1:WP_076482575.1
          Length = 507

 Score =  301 bits (772), Expect = 3e-86
 Identities = 180/472 (38%), Positives = 257/472 (54%), Gaps = 17/472 (3%)

Query: 12  VSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLA 71
           V G+  + P  +P  G    EIA ++AE +D A+ AA  A   WG+T P  R+  LL++A
Sbjct: 32  VKGQYFENP--SPINGRTFCEIARSTAEDIDLALDAAHKAAPAWGKTAPAERSLVLLRIA 89

Query: 72  DVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHT 131
           D IEEN +  A  ES + GK +      +IP  VD  R+FAGA R   G +  E  E   
Sbjct: 90  DRIEENLEKIAVAESWDNGKAVRETLAADIPLAVDHLRYFAGALRAQQG-SISEIDEDTV 148

Query: 132 SMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI 191
           +    +PLGVV  I PWN+P++MA WK+APALAAGN +VLKP+E TP + L L  L  D+
Sbjct: 149 AYHFHEPLGVVGQIIPWNFPILMAIWKIAPALAAGNAIVLKPAEQTPASILYLISLIGDL 208

Query: 192 FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKA 251
            P GV+N++ G G   G PL    ++R ++ TG   TG  I+ + + +I    +ELGGK+
Sbjct: 209 LPEGVLNVVNGFGVEAGKPLASSNRIRKIAFTGETTTGRLIMQYASENIIPVTLELGGKS 268

Query: 252 PVIVFDDADI------EAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVA 305
           P I FDD  I      +  +EG   F   N G+ CT   R   Q+GIYD  +E     V 
Sbjct: 269 PNIFFDDVLIADDGFRQRALEGFAMFA-LNQGEVCTCPSRALIQEGIYDDFIELGVERVK 327

Query: 306 TLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-----GNGYYY 360
            +K G P D  T +G  +S    E++   +   K  G  +V+TGGE  +       GYY 
Sbjct: 328 HIKQGNPLDTETMMGAQASNDQFEKITSYLSIGKEEG-AEVLTGGEILELDGDLAGGYYI 386

Query: 361 APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR 420
            PT+ AG+     I Q+E+FGPV+SV  F +  + ++ AND+ YGL + VW++D   A+R
Sbjct: 387 KPTVFAGS-NKMRIFQEEIFGPVLSVAKFADYNEAMSIANDTLYGLGAGVWSRDGATAYR 445

Query: 421 VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472
               +Q G  W NT+    +    GG K SG G++  L  LE Y   ++++V
Sbjct: 446 AGREIQAGRVWTNTYHDYPAHAAFGGYKQSGIGRENHLVMLEHYQQTKNLLV 497


Lambda     K      H
   0.317    0.134    0.397 

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: 574
Number of extensions: 30
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: 474
Length of database: 507
Length adjustment: 34
Effective length of query: 440
Effective length of database: 473
Effective search space:   208120
Effective search space used:   208120
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 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