Alignments for a candidate for adhAqn in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Azospirillum brasilense Sp245

Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate AZOBR_RS24625 AZOBR_RS24625 methanol dehydrogenase

Query= BRENDA::Q44002
         (739 letters)



>FitnessBrowser__azobra:AZOBR_RS24625
          Length = 627

 Score =  319 bits (817), Expect = 3e-91
 Identities = 211/600 (35%), Positives = 299/600 (49%), Gaps = 48/600 (8%)

Query: 30  ATMASADDGQGATGEAIIHADDHPGNWMTYGRTYSEQRYSPLDQINRSNVGNLKLAWYLD 89
           A++A    G  +  ++I+  + +P NW +    Y+ QRYSPLDQI  +NV NL++AW   
Sbjct: 10  ASVAVVAAGSVSANDSILKNEANPNNWASQLGNYAGQRYSPLDQITTNNVKNLQVAWSFS 69

Query: 90  LDTNRGQEGTPLVIDGVMYATTNW-SMMKAVDAAT-GKLLWSYDPRVPGNIADKGCCDTV 147
               RG EG P+V+  VMY  T + + + A+D    G+++W Y+      +    CCDTV
Sbjct: 70  TGVLRGHEGGPIVVGDVMYIHTPFPNKVFALDLNNPGRVIWKYESVQDPTVIPVMCCDTV 129

Query: 148 NRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVNTIPPEAELGKQ-RSYTVDGAPRIAK 206
           NRG A  +GKV+    D  L+ALDAKTGK VW       +A+ G   +  T+  AP + K
Sbjct: 130 NRGVAVADGKVFLAQADNTLVALDAKTGKEVW-------KAKNGDHTKGETLTAAPLVVK 182

Query: 207 GRVIIGNGGSEFGARGFVTAFDAETGKVDWRFFTAPNPKNEPDHTASDSVLMNK------ 260
            +V +G  G EFG RG +TA+D  +GK+ WR F+   P  +     S +++M K      
Sbjct: 183 DKVFVGISGGEFGVRGHLTAYDTNSGKMVWRAFST-GPDADVKIDPSKTMMMGKPIGQKD 241

Query: 261 -AYQTWSPTGAWTRQGGGGTVWDSIVYDPVADLVYLGVGNGSPWNYKYRS----EGKGDN 315
               TW P   W R  GGGT W    YDP  +L+Y G GN   WN   R+      K DN
Sbjct: 242 LGVSTW-PGEEWKR--GGGTTWGWYTYDPALNLIYYGTGNPGTWNPTQRAVDKDRAKSDN 298

Query: 316 LFLGSIVALKPETGEYVWHFQETPMDQWDFTSVQQIMTLDLPINGETRHVIVHAPKNGFF 375
            +  +I A  P+TGE  W +Q+TP D+WDF  V + +  D+ +NG+ R V+V+  +NGF 
Sbjct: 299 KWSMTIFARDPDTGEAKWVYQKTPFDEWDFDGVNENILADINMNGQQRKVLVNFDRNGFA 358

Query: 376 YIIDAKTGEFISGKNY-VYVNWASGLDPKTGRPIYNPDALYTLTGKEWYG----IPGDLG 430
           Y +D  TGE +  + +   VNWA+ +D KTGRP    D   T    E        P  LG
Sbjct: 359 YTLDRATGELLVAQKFDPTVNWATDVDMKTGRPNV-VDKYSTFANGEDKNTAAVCPAALG 417

Query: 431 GHNFAAMAFSPKTGLVYIPAQQVPFLYTNQVGGFTPHPDSWNLGLDM--NKVGIPDSPEA 488
             +    +FSP TGL Y+P   +   Y        P   S+  G     + V +  +P +
Sbjct: 418 SKDQQPASFSPDTGLFYVPTNHICMDY-------EPFSVSYTAGQAYVGSTVSMYPTPNS 470

Query: 489 KQAFVKDLKGWIVAWDPQKQAEAW-RVDHKGPWNGGILATGGDLLFQGLANGEFHAYDAT 547
                    G  +AWD       W R +    W+G  L+T G + + G   G   A D  
Sbjct: 471 HGGM-----GNFIAWDAAAGKIVWSRPERFAVWSGA-LSTKGGVAYYGTLEGYLVAVDMK 524

Query: 548 NGSDLFHFAADSGIIAPPVTYLANGKQYVAVEVGWGGIYPFFL-GGLARTSGWTVNHSRI 606
           +G +L+ F   SGII    TY  NGKQYVAV  G GG     L  GL + +G    H+ +
Sbjct: 525 DGKELWRFKTPSGIIGNINTYTHNGKQYVAVLSGVGGWAGIGLAAGLTQEAGAQAWHNAV 584


Lambda     K      H
   0.318    0.137    0.440 

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: 1877
Number of extensions: 150
Number of successful extensions: 17
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: 739
Length of database: 627
Length adjustment: 39
Effective length of query: 700
Effective length of database: 588
Effective search space:   411600
Effective search space used:   411600
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: 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