GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Lutibaculum baratangense AMV1

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_023432018.1 N177_RS09120 aldehyde dehydrogenase

Query= BRENDA::Q97YT9
         (492 letters)



>NCBI__GCF_000496075.1:WP_023432018.1
          Length = 492

 Score =  224 bits (572), Expect = 4e-63
 Identities = 145/456 (31%), Positives = 227/456 (49%), Gaps = 3/456 (0%)

Query: 16  KLYINGEFIDSKTDTIGKAYNPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEK-WREVPIT 74
           ++ I GE+          + NP   E+ A +P +   +V  AI+ A + +   WR V   
Sbjct: 6   QMLIGGEWTGGSGSERLDSVNPYTQEVWATLPQAGDADVARAIEIAHDTYVSVWRGVNGR 65

Query: 75  TRIQYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYKGE 134
            R   L  L + +E+    +ARI   ++GK I+E    M+    N       A  L +G 
Sbjct: 66  DRALMLNRLADLVEQNGPDLARIDTTDNGKVIRETGSQMKFAARNYRYFAGLADKL-QGN 124

Query: 135 HLDQVSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVPM 194
            +   + E+ +  + EPLGV  +IT +N P  +    L  A+  GNTVV+KPSE   +  
Sbjct: 125 TIPLDNGEMLDYTIVEPLGVAVLITAWNSPLPLLANKLAPALAAGNTVVIKPSEHASIST 184

Query: 195 DFIIRIFDEIKLPRGVVNVVHGAKDVVDEFLTNKLVQGVTFVGSTRVGKYIYENAGKNGK 254
               R+  E   P GVVN+V G   +     T+K V+ ++F G     + I E A +   
Sbjct: 185 LAFGRLIAEAGFPDGVVNIVTGDGRIGPALTTHKRVKKISFTGGLPTARRILEAAARRLV 244

Query: 255 KAIVQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEVKRKFI 314
               + G K+  ++  DADL  A+   V+  FG +GQ C+A + L+   +IYDEV  + +
Sbjct: 245 PVTTELGGKSPNIIFEDADLKAAVNGAVAGIFGASGQTCIAGSRLLVQSSIYDEVCDRVL 304

Query: 315 EASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPEYPNGY 374
           E  + +++G  LD + +MGPV  +    RI+  I +   EGAKL L GR    P    G+
Sbjct: 305 EKVRGIRLGNPLDPATEMGPVANRAQFDRILSLIAQAENEGAKLALGGRQATGPGLERGF 364

Query: 375 FLGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTTSGYYA 434
           F+ PTV  +V P + IA++E+FGPV  I+  ++  +A+ I N S+YG A+ ++T     A
Sbjct: 365 FIEPTVLKDVEPSLTIARDEVFGPVLCILRFEDEADAVRIANDSDYGLAAGVWTNDVRRA 424

Query: 435 RKFRREVNTGNIGINIGVAAPMAFFPFGGRKESFFG 470
            +  RE+  G + +N    A     PFGG K S  G
Sbjct: 425 HRMAREIEAGLVWVNT-YRASYVGAPFGGTKLSGHG 459


Lambda     K      H
   0.319    0.139    0.398 

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: 555
Number of extensions: 23
Number of successful extensions: 3
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: 492
Length of database: 492
Length adjustment: 34
Effective length of query: 458
Effective length of database: 458
Effective search space:   209764
Effective search space used:   209764
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