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_013723111.1 ALIDE2_RS21420 xanthine dehydrogenase family protein molybdopterin-binding subunit

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



>NCBI__GCF_000204645.1:WP_013723111.1
          Length = 824

 Score =  332 bits (852), Expect = 4e-95
 Identities = 244/810 (30%), Positives = 398/810 (49%), Gaps = 80/810 (9%)

Query: 3   YVGKPVKRIYDDKFVTGRSTYVDDIRIPAL-YAGFVRSTYPHAIIKRIDVSDALKVNGIV 61
           ++GK +KR+ D + +TG+  Y+DDI +P + +A  +RS Y HA IK ID S A  + G++
Sbjct: 26  WIGKSMKRVEDPRLLTGKGKYIDDIVLPNMAHAALLRSPYAHARIKSIDTSRAKALPGVI 85

Query: 62  AVFTAKEINPLLKGGIRPWPTYIDIRSFRYSERKAFPENKVKYVGEPVAIVLGQDKYSVR 121
           AV T +E+    K G  P  T+      ++    A   +KV++VGE VA V+ +D+Y   
Sbjct: 86  AVVTGREMAE--KTG--PTVTFSSPPVVQH----AMAVDKVRHVGETVAAVVAEDRYIAE 137

Query: 122 DAIDKVVVEYEPLKPV---IRMEEAEKDQVIIHEELKTNISYKIPFKAGEVDKAFSESDK 178
           DA++ + VE+E L  V   +   +A  D V+  E  ++N++    F  G VD  F+ +D 
Sbjct: 138 DALELIDVEFEELPIVTDPLLQAQARGDAVLHPERGESNVAMDRTFTFGPVDDDFARADV 197

Query: 179 VVRVEAINERLIPNPMEPRGIVSRFEAGT--LSIWYSTQVPHYMRSEFARILGIPESKIK 236
           VVR +    R    P+E  G ++ ++ GT  L++  +T + +Y+    A  LGIP + + 
Sbjct: 198 VVRRKLRWNRSEAQPIETSGAIADYDEGTGKLTVHCNTSMYNYVGWLCAASLGIPATHLN 257

Query: 237 VSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLASEAR--HNVFTGEV 294
           +     GG+FG+K+ L    +   + S I GRPV++   R + M A++      V+  E+
Sbjct: 258 LVPVIAGGSFGSKLFLHKIIVLTASLSRIAGRPVKFIEDRLDHMTAADVHGCDRVYDAEL 317

Query: 295 AVKRDGTILGIKGKLLLDLGAYITVTAGIQPLIIPMMIPGPYKIRNLDIESVAVYTNTPP 354
           A+KRDGT+L ++  ++ D GAY+    G        ++ GPY+I ++    +AV +N   
Sbjct: 318 ALKRDGTMLALRYTVVDDYGAYLQYGYGTHGNTFAQIV-GPYRINSVQGRVIAVLSNKAQ 376

Query: 355 ITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVT--ELPYTNPFGLRYDSGDY 412
              YRG     + ++IER+    A ELGLD V IR +N +   E PY  P G  YDSG+Y
Sbjct: 377 QGAYRGFGSEVSNFVIERLTDAAARELGLDVVEIRRRNFIRPEEFPYLIPTGNLYDSGNY 436

Query: 413 VGLLREGVKRLGYYELKKWAEEE---RKKGHRVGVGLAYYLEICSFGPWEY--------- 460
             +L E ++    ++++ W  ++   R++G  +G+GL    E  +F   E+         
Sbjct: 437 EKVLAEALRM---FDMEGWRAKQAAARRQGRHIGIGLVTCQERSTFSATEFWSLNPPDQA 493

Query: 461 ----------AEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDT 510
                       +R+D  G V V   +   G   ET   QIVA+AL ++ S + + + DT
Sbjct: 494 GFTLTSSPEAVSMRIDPTGKVFVKLNSPFWGNSPETMATQIVAEALTVEPSDISIGYADT 553

Query: 511 DTVAASMGTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKND 570
           D+     G  GSR   +   A +   + +  K+ ++A         +++   G+  +K  
Sbjct: 554 DSGFNGTGPGGSRYTVMLAGAVVTAVKTLRGKLFKLAGHMMECAEGDLELRNGKIGVKGV 613

Query: 571 PSKKMSWDDVASIAYRSH------------DPGLVEKIIYENDVT-------------FP 605
           P+ + S   VA +A  SH              GL    +Y++ +T             +P
Sbjct: 614 PAMEKS---VAEVAIASHYFRLSFPNTPEFASGLETTAVYDHPLTTMPAADRSHLGIYYP 670

Query: 606 ---YGVHIATVEVDD-TGVARVLEYRAYDDIGKVVNPALAEAQIHGGGVQAVGQALYEQA 661
              +  H   VEVD  TG   +L+Y A  D G VVNP   +  + GG  Q +G ALYE  
Sbjct: 671 IMGHMAHATAVEVDSATGKVSILDYVAVHDCGTVVNPMTLDGHVRGGTAQGIGTALYEHY 730

Query: 662 LLNENGQLI-VTYADYYVPTAVEAPKFTSVFADQYHPSNYPTGSKGVGEAALIVGPAVII 720
             +E+GQL+  + ADY++PTA E P    +   +        G KG GE   +  PAV+ 
Sbjct: 731 RYDESGQLLTASLADYHMPTAHEMPADIRIGHVETPSPFTEFGIKGGGEGGRMATPAVLA 790

Query: 721 RALEDAIG---TRFTKTPTTPEEILRAIAS 747
           +A+EDA+     R  + P TP  +   + S
Sbjct: 791 QAVEDALSPFDVRIDEVPLTPIRLRELVRS 820


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: 1462
Number of extensions: 100
Number of successful extensions: 13
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: 824
Length adjustment: 41
Effective length of query: 708
Effective length of database: 783
Effective search space:   554364
Effective search space used:   554364
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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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