Alignments for a candidate for etoh-dh-c in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Azospirillum brasilense Sp245

Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate AZOBR_RS12740 AZOBR_RS12740 dehydrogenase

Query= CharProtDB::CH_107432
         (595 letters)



>FitnessBrowser__azobra:AZOBR_RS12740
          Length = 587

 Score =  830 bits (2145), Expect = 0.0
 Identities = 393/588 (66%), Positives = 469/588 (79%), Gaps = 16/588 (2%)

Query: 9   MFAVSLVLSAML----LAGAAHAAV------SNEEILQDPKNPQQIVTNGLGVQGQRYSP 58
           +F   L+ SAM     L+G A AA        N+++L D  +   ++T G+G Q QR+SP
Sbjct: 4   LFRTCLLASAMAAGLGLSGPALAAAPVAGGPGNDDLLNDATSTGDVLTYGMGPQAQRFSP 63

Query: 59  LDLLNANNVKELRPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSRVFAVDARTGKKLW 118
           LD LN + VK L PVW+FSFGGEKQRGQ++QPLI DG +Y+TGSYSR++AVD +TG+K W
Sbjct: 64  LDKLNPDTVKGLVPVWSFSFGGEKQRGQESQPLIHDGTIYVTGSYSRLYAVDVKTGQKKW 123

Query: 119 QYDARLPDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGY 178
           QYD RLP+ I PCCDV+NRG ALY D ++F TLDA+LVALNKDTGKVVWSKK+ D+K GY
Sbjct: 124 QYDHRLPEGIMPCCDVVNRGAALYKDKIYFATLDARLVALNKDTGKVVWSKKIEDYKAGY 183

Query: 179 SISAAPMIVNGKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIE 238
           S +AAP+IV+GK+ITG +GGEFG++G ++A + E GEL+W RPT+EG+MG +  +GK   
Sbjct: 184 SATAAPLIVDGKVITGNSGGEFGIIGMVEARDAETGELVWQRPTIEGNMGTL--NGK--- 238

Query: 239 NGISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLRPGDNLYSS 298
                G    +W GDL+KTGG A WLGG YDPET  + FGTGNPAPWNSHLRPGDNLY+S
Sbjct: 239 ESTMTGVMNASWSGDLYKTGGGATWLGGTYDPETKTLFFGTGNPAPWNSHLRPGDNLYTS 298

Query: 299 SRLALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFFYVLD 358
           S LA++P +G IKWH+Q+TPHDGWDFDGVNEL+SF+ K  G+ +KA A ADRNGFFYVLD
Sbjct: 299 STLAIDPANGDIKWHYQTTPHDGWDFDGVNELVSFDLKKDGQTIKAGAKADRNGFFYVLD 358

Query: 359 RTNGKFIRGFPFVDKITWATGLD-KDGRPIYNDASRPGAPGSEAKGSSVFVAPAFLGAKN 417
           RTNGK +   PFV KITWA  +D K GRP+YND +RPG P    KG+SVF APAFLGAKN
Sbjct: 359 RTNGKLLSASPFVTKITWAKEIDVKTGRPVYNDDNRPGTPVGAEKGTSVFAAPAFLGAKN 418

Query: 418 WMPMAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDP 477
           WMPMAY+  T LFYVP+NEWGMDIWNE I YKKGAA+LGAGFTIKPL +DYIG LRAIDP
Sbjct: 419 WMPMAYSPATELFYVPANEWGMDIWNEPITYKKGAAYLGAGFTIKPLYDDYIGALRAIDP 478

Query: 478 ISGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGVLGSP 537
            +GK VW +KN APLWGGVLTT GNLVFTGTPEG+L+AF+AK+G +VW+F TGSGV+GSP
Sbjct: 479 KTGKIVWEYKNPAPLWGGVLTTGGNLVFTGTPEGYLKAFDAKSGKEVWKFNTGSGVVGSP 538

Query: 538 VTWEMDGEQYVSVVSGWGGAVPLWGGEVAKRVKDFNQGGMLWTFKLPK 585
           VTWE DGEQYV+VVSGWGGAVPLWGG+VAK VKD NQGG LW FKLPK
Sbjct: 539 VTWEQDGEQYVAVVSGWGGAVPLWGGDVAKLVKDINQGGSLWVFKLPK 586


Lambda     K      H
   0.317    0.137    0.438 

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: 1821
Number of extensions: 133
Number of successful extensions: 14
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: 595
Length of database: 587
Length adjustment: 37
Effective length of query: 558
Effective length of database: 550
Effective search space:   306900
Effective search space used:   306900
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: 53 (25.0 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:

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
the source code
instructions for running GapMind on your computer

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