GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Marinobacter adhaerens HP15

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate GFF4092 HP15_4032 betaine aldehyde dehydrogenase

Query= reanno::Caulo:CCNA_01360
         (500 letters)



>FitnessBrowser__Marino:GFF4092
          Length = 486

 Score =  227 bits (579), Expect = 6e-64
 Identities = 158/491 (32%), Positives = 246/491 (50%), Gaps = 22/491 (4%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVA-QAAWAA 60
           M+DI H+I GQ V  ASGR  +  +P  GKV ++V  A   E++ A+  A+ A +  W  
Sbjct: 1   MKDIKHYINGQYVGSASGRLFDNVNPANGKVISKVHEAGREEVDAAVKAARAALRGPWGK 60

Query: 61  TNPQRRARVMFEFKRLLEVHMDEL--AALLSSEHGKVIADSKGDIQRGLEVIE-FACGVP 117
              ++R  ++ +    +    DE   A  L +   K +A S  DI RG    + FA  + 
Sbjct: 61  MTLEQRTAILHKVADGINARFDEFLEAECLDTGKPKSLA-SHIDIPRGAANFKVFADMIK 119

Query: 118 HLLKGEYTQGA--GPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKP 175
           ++    +      G G   Y++R+P GV+  I+P+N P ++  W  GPA+A GN  ++KP
Sbjct: 120 NVPTESFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKP 179

Query: 176 SERDPSVPVRLAELMIEAGLPPGVLNVVHG-DKDCVEAIL-DHPDIKAVSFVGSSDIAQS 233
           SE  P+    L E+M EAG+P GV NVVHG   D   A L +HP +   +F G +   + 
Sbjct: 180 SEETPTTTALLGEVMKEAGVPDGVYNVVHGFGGDSAGAYLTEHPQVDGFTFTGETGTGEV 239

Query: 234 VFQRAGAAGKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGE 293
           + + A    + +    G KN GLV  D D+++A+   + +A+ + G+ C+    V  V  
Sbjct: 240 IMKAAAKGIRDISLELGGKNAGLVFADCDMEKAIEGTMRSAFANCGQVCLGTERVY-VER 298

Query: 294 KTATALREKLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGR 353
                   +L  A  GL++G   D DA+ GP+VS  H+ ++ SY Q  VD+GA +V  G 
Sbjct: 299 SIFDEFVGRLKEAAEGLKIGPPDDADANLGPLVSLKHREKVLSYYQKAVDDGATVVTGGG 358

Query: 354 GFSLQGH-EEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGN 412
              +      G +V PT++  +   S    DEIFGP   +   ++ EE I LA+   YG 
Sbjct: 359 VPDMPAELAGGAWVEPTIWTGLPDDSAVVTDEIFGPCCHIRPFDTEEEAIELANSLPYGL 418

Query: 413 GVAIFTRNGDAAREFADQVEVGMVGINV----PIPVPVAYHSFGGWKRSGFGDLNQYGMD 468
             AI++ N   A   A Q+E G++ +N      +  P     FGG K+SG G   + G+ 
Sbjct: 419 ASAIWSENITRAHRVAGQIEAGIIWVNSWFLRDLRTP-----FGGSKQSGVG--REGGVH 471

Query: 469 GVRFYTRTKTV 479
            + FYT  K +
Sbjct: 472 SLEFYTEMKNI 482


Lambda     K      H
   0.320    0.137    0.409 

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: 663
Number of extensions: 42
Number of successful extensions: 5
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: 500
Length of database: 486
Length adjustment: 34
Effective length of query: 466
Effective length of database: 452
Effective search space:   210632
Effective search space used:   210632
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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