Alignments for a candidate for aldox-large in Alicycliphilus denitrificans K601

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Alicycliphilus denitrificans K601

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate WP_013518812.1 ALIDE2_RS11080 xanthine dehydrogenase family protein molybdopterin-binding subunit

Query= metacyc::MONOMER-18071
         (749 letters)



>NCBI__GCF_000204645.1:WP_013518812.1
          Length = 790

 Score =  455 bits (1170), Expect = e-132
 Identities = 292/784 (37%), Positives = 423/784 (53%), Gaps = 42/784 (5%)

Query: 1   MSYVGKPVKRIYDDKFVTGRSTYVDDIRIPAL-YAGFVRSTYPHAIIKRIDVSDALKVNG 59
           + ++G+ VKR  D +F+TG   Y DDI  P   YA FVRS Y HA IK +D + A  + G
Sbjct: 9   LPHIGESVKRKEDLRFLTGAGNYTDDIVQPGQKYAVFVRSPYAHANIKSVDTAAAAAMPG 68

Query: 60  IVAVFTAKEINPLLKGGIRPWP-TYIDIRSFRYSERKAFPENKVKYVGEPVAIVLGQDKY 118
           + AVFT K+I   + G    W  +  D    +          KV+YVG+ VA+V+     
Sbjct: 69  VAAVFTGKDIEGKVNGLPCGWLISNPDGSPMKEPPHPVLASTKVRYVGDHVAMVVADTLE 128

Query: 119 SVRDAIDKVVVEYEPLKPVIRMEEAEKDQVIIHEELKTNISYKIPF-KAGEVDKAFSESD 177
             ++A + V V+YE L PVI M  A +   + H E   N  YK        VD AF+ + 
Sbjct: 129 QAKNAAEAVAVDYEELAPVIDMRTASQGPAL-HAEAPDNHCYKWTLGDKAAVDAAFAGAA 187

Query: 178 KVVRVEAINERLIPNPMEPRGIVSRFEAGT--LSIWYSTQVPHYMRSEF-ARILGIPESK 234
            V  ++  N RLIPN MEPR   + +   T    ++ + Q PH  R    A +LG+PE K
Sbjct: 188 HVTAIDLTNNRLIPNAMEPRAANASYNRATDEYQLYVANQNPHVERLLMTAFVLGLPEHK 247

Query: 235 IKVSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNVFTGE 293
           ++V  PDVGG FG+K+ L  E++A+  ++  L  P++WTA RSE  ++ +  R ++   E
Sbjct: 248 VRVIAPDVGGGFGSKIFLYAEDVALTWAARQLNCPIKWTAERSESFVSDAHGRDHISHAE 307

Query: 294 VAVKRDGTILGIKGKLLLDLGAYITVTAGIQPLII-PMMIPGPYKIRNLDIESVAVYTNT 352
           +A+ +DG  L ++     +LGAY++  A   P I+   ++ G Y    + +E    +T+T
Sbjct: 308 MAMDKDGKFLAMRVHTHANLGAYLSTFASAIPTILYGTLLAGQYATPQIYVEVDGWFTST 367

Query: 353 PPITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVTELPYTNPFGLRYDSGDY 412
            P+  YRGA RPEA Y++ER+++  A ELGL    IR++N +   PY  P  L+YD+GD+
Sbjct: 368 APVDAYRGAGRPEAAYLVERLVTRCAWELGLPQDEIRKRNFIASFPYQTPVALQYDTGDF 427

Query: 413 VGLLREGVKR--LGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGP------------- 457
              + E  K   +  +E ++ A E R  G R G+G + Y+E C   P             
Sbjct: 428 HACMNESQKLADVAGFEARRKASEAR--GLRRGMGYSCYIEACGLAPSNIAGALGARAGL 485

Query: 458 WEYAEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAASM 517
           +E  EVRV   G V V TG+  HGQG ET  AQ+VA  L +D  +V ++ GDT  V   M
Sbjct: 486 FEAGEVRVHPTGSVTVFTGSHSHGQGHETTFAQLVAARLGLDPGQVDIVHGDTGRVPFGM 545

Query: 518 GTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMSW 577
           GTYGSRS+++GG+A +K  +KI  K K+IAA        ++++  GEF +K    KK+ +
Sbjct: 546 GTYGSRSLSVGGTAIMKALDKIEAKAKKIAAHLMEASDADIEFAGGEFTVKG-TDKKVPF 604

Query: 578 DDVASIAYRSH-------DPGLVEKIIYE-NDVTFPYGVHIATVEVD-DTGVARVLEYRA 628
             VA  AY  H       +PGL E   Y+  + T+P G +I  VEVD  TGV RV  + A
Sbjct: 605 AQVALTAYVPHNYPLDKLEPGLNETAFYDPTNFTYPAGTYICEVEVDPQTGVVRVDRFTA 664

Query: 629 YDDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLN-ENGQLIV-TYADYYVPTAVEAPK 686
            DD G +VNP + E Q+HGG VQ +GQAL E  + + ++GQL+  +Y DY +P A + P+
Sbjct: 665 VDDFGVIVNPMIVEGQVHGGVVQGMGQALMEHGVYDPDSGQLLTGSYMDYTMPRAADFPE 724

Query: 687 FTSVFADQYHPSNYPTGSKGVGEAALIVGPAVIIRALEDA---IGTRFTKTPTTPEEILR 743
           F           N P GSKG GEA  I  P  +I A+ DA   +G      P TP  + +
Sbjct: 725 FKLGHVCTPCTHN-PIGSKGCGEAGAIGSPPAVINAVLDALRPLGVTDIDMPATPHRVWQ 783

Query: 744 AIAS 747
           AI S
Sbjct: 784 AIQS 787


Lambda     K      H
   0.317    0.136    0.394 

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: 1455
Number of extensions: 78
Number of successful extensions: 11
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: 749
Length of database: 790
Length adjustment: 41
Effective length of query: 708
Effective length of database: 749
Effective search space:   530292
Effective search space used:   530292
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: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
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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