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 alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate AZOBR_RS27870 AZOBR_RS27870 quinoprotein ethanol dehydrogenase

Query= BRENDA::Q9Z4J7
         (623 letters)



>FitnessBrowser__azobra:AZOBR_RS27870
          Length = 640

 Score =  962 bits (2486), Expect = 0.0
 Identities = 450/595 (75%), Positives = 502/595 (84%), Gaps = 20/595 (3%)

Query: 30  GAALAKDVTWEDIANDDKTTGDVLQYGMGTHAQRWSPLKQVNADNVFKLTPAWSYSFGDE 89
           G+A A DVTW+DIAND K+ GDVL YGMG   +R+SPLKQ++ ++V +L PAWS+SFGDE
Sbjct: 46  GSAQAADVTWDDIANDAKSAGDVLMYGMGVEGKRFSPLKQIDTNSVSRLVPAWSFSFGDE 105

Query: 90  KQRGQESQAIVSDGVIYVTASYSRLFALDAKTGKRLWTYNHRLPDDIRPCCDVVNRGAAI 149
           KQRGQE+QA+V DGVIYVTASYSR+FALDA+TGKRLWTY HRLPDDIRPCCDVVNRGAAI
Sbjct: 106 KQRGQETQALVHDGVIYVTASYSRMFALDARTGKRLWTYAHRLPDDIRPCCDVVNRGAAI 165

Query: 150 YGDKVFFGTLDASVVALNKNTGKVVWKKKFADHGAGYTMTGAPTIVKDGKTGKVLLIHGS 209
           YGDKVFFGTLDAS+VALNK+TGKVVW+KKFADH  GYTMTGAPT+VKD KTG++LLIHGS
Sbjct: 166 YGDKVFFGTLDASIVALNKDTGKVVWRKKFADHKVGYTMTGAPTVVKDQKTGRMLLIHGS 225

Query: 210 SGDEFGVVGRLFARDPDTGEEIWMRPFVEGHMGRLNGKDSTVTGDVKAPSWPDDRNSPTG 269
           SGDEFGVVGRLFARDPDTG+EIWMRP VEGHMGRL+GKDST TG+ KAPSWP D++    
Sbjct: 226 SGDEFGVVGRLFARDPDTGDEIWMRPLVEGHMGRLDGKDSTPTGNAKAPSWPRDKDGQL- 284

Query: 270 KVESWSHGGGAPWQSASFDAETNTIIVGAGNPGPWNTWARTAKGGNPHDYDSLYTSGQVG 329
            VE+W+HGGGAPWQSA+FD ETNTI++G GNP PWN WAR          DSLYTSGQ  
Sbjct: 285 -VEAWNHGGGAPWQSATFDVETNTIVIGTGNPAPWNGWARWPG-------DSLYTSGQAY 336

Query: 330 VDPSSGEVKWFYQHTPNDAWDFSGNNELVLFDYKAKDGKIVKATAHADRNGFFYVVDRSN 389
           VDP++GE+K FYQHTPND WDFSGNNELVLFDYK   GK VKATAHADRNGFFYV DR+ 
Sbjct: 337 VDPTTGELKGFYQHTPNDTWDFSGNNELVLFDYKDASGKTVKATAHADRNGFFYVTDRTK 396

Query: 390 -----------GKLQNAFPFVDNITWASHIDLKTGRPVEREGQRPPLPEPGQKHGKAVEV 438
                        +  AFPFVD ITWA  IDLKTGRP+E EGQRPP P  G+K GKAVEV
Sbjct: 397 LATAGGEANKPNSVLAAFPFVDGITWAKGIDLKTGRPIEVEGQRPPPPAEGEKRGKAVEV 456

Query: 439 SPPFLGGKNWNPMAYSQDTGLFYVPANHWKEDYWTEEVSYTKGSAYLGMGFRIKRMYDDH 498
           SPPFLGGKNWNPM+YS+DTGLFY+ ANHWKEDYWTE V Y  GSAYLGMGFRI +M++DH
Sbjct: 457 SPPFLGGKNWNPMSYSEDTGLFYIAANHWKEDYWTEHVGYNPGSAYLGMGFRIHKMFEDH 516

Query: 499 VGSLRAMDPVSGKVVWEHKEHLPLWAGVLATAGNLVFTGTGDGYFKAFDAKSGKELWKFQ 558
           VG LRA+DP +GKV WEHKE LPLW+G LATAG LVFTGTGDGY KAFDAKSG ELWKFQ
Sbjct: 517 VGVLRAIDPTTGKVAWEHKEELPLWSGTLATAGGLVFTGTGDGYVKAFDAKSGAELWKFQ 576

Query: 559 TGSGIVSPPITWEQDGEQYLGVTVGYGGAVPLWGGDMADLTRPVAQGGSFWVFKL 613
           TGSGI+S P+TWE DG QY+G+T GYGGAVPLWGGD+ADLT  V QGGSFWVFKL
Sbjct: 577 TGSGIISSPVTWELDGVQYVGITTGYGGAVPLWGGDLADLTTRVTQGGSFWVFKL 631


Lambda     K      H
   0.316    0.135    0.436 

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: 1989
Number of extensions: 154
Number of successful extensions: 16
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 623
Length of database: 640
Length adjustment: 38
Effective length of query: 585
Effective length of database: 602
Effective search space:   352170
Effective search space used:   352170
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: 54 (25.4 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