GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Methanospirillum lacunae Ki8-1

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_109968015.1 DK846_RS05900 aldehyde dehydrogenase family protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_1229
         (505 letters)



>NCBI__GCF_003173355.1:WP_109968015.1
          Length = 473

 Score =  188 bits (477), Expect = 4e-52
 Identities = 142/473 (30%), Positives = 223/473 (47%), Gaps = 18/473 (3%)

Query: 21  VESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGARMRIMLKL 80
           VE ++ + + +VNP + +V+ +V   +A +++ A+ AA              R  ++ +L
Sbjct: 11  VERRSEDRYLVVNPFSGEVVGQVSRCSAEDIEEALQAATAGSTVTAELAAHQRATVLRRL 70

Query: 81  QALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVV----EHACSIGSLQMGEFAENVA 136
             L+  H +    +L  E GK   +AEG+  R +E +    E A  IG  ++      V 
Sbjct: 71  VDLMTAHREEFITLLIAEGGKPRRNAEGETARAIETILISAEEAVRIGG-EVIPLDRTVP 129

Query: 137 G-GVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTMLLVE 195
           G G      R P+GV  GITPFNFP  +       A+A GN  +LKP+   P+S++LL  
Sbjct: 130 GEGCIGIVQRFPVGVVLGITPFNFPLNLACHKLGPAVASGNAIILKPASATPLSSLLLGR 189

Query: 196 LAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKRVQSM 255
           L +EAG PP  ++V+    D  + L   + I   SF GS  VG H+   A     +V   
Sbjct: 190 LLLEAGYPPAAVSVLICSPDDAERLAADQRIGCFSFTGSPEVGWHLRSRATY--AKVTLE 247

Query: 256 MGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATS-VVVLVGAAKQWLPDLKALAQK 314
           +G     +V  D +   A + ++  GF  AGQ C++   V V     +  L  L  LA  
Sbjct: 248 LGGNGAVIVHEDCDLSHAASRIIEGGFSQAGQVCISVQRVFVHRPVFEPLLTRLGELADG 307

Query: 315 LKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGNFVGPT 374
           L V   S+P TDVG +ISK A    L  I+     GA L + G  +S      G+ + PT
Sbjct: 308 LVVGDPSDPKTDVGSMISKEAAEHALKRIQDACSAGATL-IKGGSLS------GSLLQPT 360

Query: 375 LFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARKFQT 434
           + +G    M++  +E+F P++ V   DT +QA+A VN + +G   G+FT+     R   +
Sbjct: 361 ILTGTKAGMEVNCREVFAPIITVTPYDTFEQAVADVNDSVYGLQAGVFTRDLLRVRYAFS 420

Query: 435 EIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTAR 487
            + VG V I       V    + G + S  G  GP  +  ++  T T+ +  R
Sbjct: 421 HLKVGTVVIGDIPTFRVDMMPYGGVKRSGSGREGP--RYAIEEMTDTRMMIIR 471


Lambda     K      H
   0.319    0.135    0.397 

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: 515
Number of extensions: 23
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: 505
Length of database: 473
Length adjustment: 34
Effective length of query: 471
Effective length of database: 439
Effective search space:   206769
Effective search space used:   206769
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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:

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:

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:

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:

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