Alignments for a candidate for adhAqn in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Sinorhizobium fredii NGR234

Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate WP_012706388.1 NGR_RS01590 PQQ-dependent methanol/ethanol family dehydrogenase

Query= BRENDA::P18278
         (742 letters)



>NCBI__GCF_000018545.1:WP_012706388.1
          Length = 588

 Score =  318 bits (815), Expect = 5e-91
 Identities = 196/572 (34%), Positives = 290/572 (50%), Gaps = 46/572 (8%)

Query: 56  LSYGRTYSEQRYSPLDQINRSNVGDLKLLGYYTL--DTNRGQEATPLVVDGIMYATTNWS 113
           L+ G     QRYSPL+ +N++NV +L     ++L  +  RGQE+ P+V DG+MY T ++S
Sbjct: 38  LTNGMGRGLQRYSPLETLNKTNVKNLLPAWGFSLGGEKQRGQESQPIVYDGVMYITASYS 97

Query: 114 KMEALDAATGKLLWQYDPKVPGNIADKGCCDTVNRGAGYWNGKVFWGTFDGRLVAADAKT 173
           ++ A+D  TGK LWQ+D ++P  I    CCD +NRGA  +   +++GT D RLVA + KT
Sbjct: 98  RLYAIDIKTGKELWQFDARLPEGILP--CCDVINRGAAIYGDNIYFGTLDARLVALNRKT 155

Query: 174 GKKVWAVNTIPADASLGKQRSYTVDGAVRVAKGLVLIGNGGAEFGARGFVSAFDAETGKL 233
           G  VW  N   A+   G    Y+   A  +  GL++ GN G EFG  G V A DA+TG+L
Sbjct: 156 GDVVW--NKKIANYKEG----YSYTAAPLIVNGLIITGNSGGEFGIVGEVQARDAKTGEL 209

Query: 234 KWRFYTVPNNKNEPDHAASDNILMNKAYKTWGPKGAWVRQGGGGTVWDSLVYDPVSDLIY 293
            W    +  +     +   D+ +      TW P   W  + GGG  W    YD  +D + 
Sbjct: 210 VWTRPVIEGHVGS--YKGKDSSMTGTLNATW-PGDLW--KTGGGATWLGGSYDADTDTLV 264

Query: 294 LAVGNGSPWNYKYRSEGI------GSNLFLGSIVALKPETGEYVWHFQATPMDQWDYTSV 347
              GN +PWN   R+ G       G NL+  S + + PE GE  WHFQ TP + WD+  V
Sbjct: 265 FGTGNPAPWNSHLRNAGKPVEGNKGDNLYAASRLGINPENGEIKWHFQTTPREGWDFDGV 324

Query: 348 QQIMTLDMPVKGEMRHVIVHAPKNGFFYVLDAKTGEFLSGKNYVYQ-NWANGLDPLTGRP 406
            +++     +  +       A +NGFFYVL+ + G+F++   +V    WA G+D  TGRP
Sbjct: 325 NEVVPF---ISKDGTKRFATADRNGFFYVLNREDGKFVAAYPFVKNITWAKGIDE-TGRP 380

Query: 407 MY---NPDGLYTL-----NGKFWYGIPGPLGAHNFMAMAYSPKTHLVYIPAHQIPFGYKN 458
           +Y   N  G  +       G+  + +P  LG  N+M MAYS K+ L Y+P+++      N
Sbjct: 381 IYAEENRPGDPSSAADGGKGQQVFSVPSFLGGKNWMPMAYSQKSELFYVPSNEWGMDIWN 440

Query: 459 QVGGFKPHADSWNVGLDMTKNGLPDTPEARTAYIKDLHGWLLAWDPVKMETVWKIDHKGP 518
           +   +K  A     G  +                +D  G L A DP   E  W+  +  P
Sbjct: 441 EPISYKKGAAYLGAGFTIKP------------LFEDYIGSLKAIDPNSGEIKWEYKNAAP 488

Query: 519 WNGGILATGGDLLFQGLANGEFHAYDATNGSDLYKFDAQSGIIAPPMTYSVNGKQYVAVE 578
             GG++AT G L+F G   GEF A D   G +L+ F   SG++  P+T+  +G+QYV+V 
Sbjct: 489 LWGGVMATAGGLVFVGTPEGEFKALDDETGEELWSFQTGSGVVGQPITWEQDGEQYVSVI 548

Query: 579 VGWGGIYPISMGGVGRTSGWTVNHSYIAAFSL 610
            GWGG  P+  G V +   +      +  F L
Sbjct: 549 SGWGGAVPLWGGEVAKKVNYLNQGGMVWTFRL 580


Lambda     K      H
   0.318    0.137    0.439 

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: 1715
Number of extensions: 146
Number of successful extensions: 20
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: 742
Length of database: 588
Length adjustment: 38
Effective length of query: 704
Effective length of database: 550
Effective search space:   387200
Effective search space used:   387200
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 Apr 09 2024. 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 2024 update 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