Alignments for a candidate for pad-dh in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for pad-dh in Azospirillum brasilense Sp245

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase

Query= BRENDA::V4GH04
         (496 letters)



>FitnessBrowser__azobra:AZOBR_RS22315
          Length = 497

 Score =  325 bits (832), Expect = 3e-93
 Identities = 190/487 (39%), Positives = 278/487 (57%), Gaps = 15/487 (3%)

Query: 13  LPHQMLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRR 72
           L  +   GG++  A SGK   V NPATG+ + E   G+  DV+AAV +A A  +   W +
Sbjct: 18  LSSKHFFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAAQKE--WAK 75

Query: 73  MPPSARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATK 132
            P   R +++     +L+ H +E+A+L  L  GK L     +E G  +    +  G A +
Sbjct: 76  RPVRERGKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPE 135

Query: 133 LTGSTLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLK 192
           L G T+    P  P + +   T R PVGVV AIIPWN PLL+   KIAPA+  GN VV+K
Sbjct: 136 LKGETI----PFNPSMLTM--TVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVK 189

Query: 193 PAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRI 252
            AEE PL  LR+ +L +   +PAG +N+++G G   G  LV H  V KV FTGS E G+I
Sbjct: 190 SAEEAPLAVLRVVQL-INTVIPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKI 248

Query: 253 IGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAI-FFNHGQVCTAGSRLYVHE 311
           +       L  V+LELGGKSP+IV  D D  +A  GA A + F   GQ CTA SR++VH+
Sbjct: 249 VYKTAAEKLIPVTLELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHD 308

Query: 312 SIYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADL-ICGG 370
           SI++  +++L     ++ +G  L++   +G +VS +  + V  +I  G E GA   +C  
Sbjct: 309 SIHDAFVEKLKEKVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSA 368

Query: 371 --TEAPCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGL 428
             ++    +G +V+P IF   +  D R+  +E+FGPV     ++D  EV+ +AN + YGL
Sbjct: 369 MPSDPKLTKGLYVQPHIFTGVKNSD-RIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGL 427

Query: 429 GASIWTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHG-AAAIEHYT 487
            A+IWT DL  A+     LEAG V VN + +V PNL +GG K SG+G+E    A +EH+T
Sbjct: 428 AATIWTRDLKVAMDAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAMLEHFT 487

Query: 488 TTRSLVI 494
             ++++I
Sbjct: 488 HKKTIII 494


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: 577
Number of extensions: 25
Number of successful extensions: 6
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: 497
Length adjustment: 34
Effective length of query: 462
Effective length of database: 463
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources