Alignments for a candidate for aldA in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Hydrogenophaga taeniospiralis NBRC 102512

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_068170336.1 HTA01S_RS10225 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase

Query= reanno::Smeli:SMc02322
         (699 letters)



>NCBI__GCF_001592305.1:WP_068170336.1
          Length = 701

 Score =  895 bits (2312), Expect = 0.0
 Identities = 447/696 (64%), Positives = 536/696 (77%), Gaps = 16/696 (2%)

Query: 14  WDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWVKGSG 73
           WDD   AGM +P  LLYRSNLLGSD RITNYGGGNTSAK+ ++DPL+G   EVLWVKGSG
Sbjct: 12  WDDAATAGMDQPHLLLYRSNLLGSDLRITNYGGGNTSAKIWQRDPLSGADAEVLWVKGSG 71

Query: 74  GDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTPLHAY 133
           GDVG++K+DGFSTLYMDKLRALKG+YRG+E EDEMVGYLPHCTFNLN RAASIDTPLH+ 
Sbjct: 72  GDVGSMKLDGFSTLYMDKLRALKGLYRGLEHEDEMVGYLPHCTFNLNARAASIDTPLHSS 131

Query: 134 VPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQENPD 193
           +P  HVDHMHPDA+IAIAA  N   +T +++   +GW+PW RPGYELG  L  +   +P 
Sbjct: 132 LPYAHVDHMHPDAVIAIAAMANGEAITRQVYEGTVGWMPWLRPGYELGQRLAAYNAAHPG 191

Query: 194 ARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTG---PAFGGRSKPVLAAAD 250
            RG+VL  HGLF+WG++++  YE T+++I RA AW   E        FGG     L  A 
Sbjct: 192 LRGIVLGGHGLFSWGESSRACYENTVDLIERAQAWLSRERERRQVQVFGGTRFDTLDGAA 251

Query: 251 RAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRTKI 310
             A   +++PV+RGL + G  K+ H + S  V+ FV S  LEPLAALGTSCPDHFLRTKI
Sbjct: 252 SEATLARVLPVLRGLAAQGSPKLLHVNTSPEVMQFVNSAELEPLAALGTSCPDHFLRTKI 311

Query: 311 RPLVVDFDPAQPDVGNTLAG------LPEAIATYRADYAAYYERCKRADSPAMRDPNAVV 364
           RPL+V      P+   TL G      L + +  YRADYAAYYERCKRA+SPA+RDPN VV
Sbjct: 312 RPLIV------PEAVYTLEGPALKTALDDLLTAYRADYAAYYERCKRANSPALRDPNPVV 365

Query: 365 YLVPGVGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEA 424
            L+P +GM+T AKDKATARI+ EFYVNAINVMR A+ V  YVGLPEQEAFDIEYWLLEEA
Sbjct: 366 ILLPRIGMVTIAKDKATARIAGEFYVNAINVMREANAVDQYVGLPEQEAFDIEYWLLEEA 425

Query: 425 KLQRMPKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTR 484
           KLQRMPKPK L G++ALVTGGAGGIG+A A R++ EGACVVLADIDE AL +   +L+  
Sbjct: 426 KLQRMPKPKPLVGKVALVTGGAGGIGQAIARRMLAEGACVVLADIDEDALASVTADLAKA 485

Query: 485 YGKDFVRSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNM 544
           +GKD VR V  +VT EA+V + +G A LAFGG+DILVSNAG+A++A +++TTLALWN+N 
Sbjct: 486 HGKDHVRGVRCDVTDEASVIAAYGRAALAFGGVDILVSNAGIASAAPIDETTLALWNRNQ 545

Query: 545 DILATGYFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLA 604
            ILATGYFLV+REAF++ + Q  GG++V +ASKNG+ AS  A+AYC AKAAEI L+R  A
Sbjct: 546 SILATGYFLVAREAFKLMKAQGTGGSIVMIASKNGMVASNQATAYCAAKAAEIQLSRSFA 605

Query: 605 LEGASAQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLKLSVFP 664
           LEGA   IR NVVNPDAV+RGSKIWTG+W E+RAAA K+D  +LEA YR+RSMLK SVFP
Sbjct: 606 LEGAPLGIRSNVVNPDAVIRGSKIWTGKWSEERAAANKVDEGDLEAFYRDRSMLKRSVFP 665

Query: 665 EDIAEAIYFLA-SDMSAKSTGNIVNVDAGNAQSFTR 699
           EDIAEA YF A  D+SAKSTGNI+NVDAGN  +FTR
Sbjct: 666 EDIAEATYFFACEDLSAKSTGNILNVDAGNLAAFTR 701


Lambda     K      H
   0.317    0.133    0.393 

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: 1301
Number of extensions: 43
Number of successful extensions: 4
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: 699
Length of database: 701
Length adjustment: 39
Effective length of query: 660
Effective length of database: 662
Effective search space:   436920
Effective search space used:   436920
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 24 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