GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Marinobacter adhaerens HP15

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF4092 HP15_4032 betaine aldehyde dehydrogenase

Query= BRENDA::Q1XGK8
         (486 letters)



>lcl|FitnessBrowser__Marino:GFF4092 HP15_4032 betaine aldehyde
           dehydrogenase
          Length = 486

 Score =  869 bits (2245), Expect = 0.0
 Identities = 414/486 (85%), Positives = 452/486 (93%)

Query: 1   MKEIKHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGK 60
           MK+IKH+ING +VGSASGR F+++NP+NG+VI  VHEAGR EVDAAVKAARAAL+GPWGK
Sbjct: 1   MKDIKHYINGQYVGSASGRLFDNVNPANGKVISKVHEAGREEVDAAVKAARAALRGPWGK 60

Query: 61  LSVAERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKN 120
           +++ +R  ILH+VADGI ARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFAD++KN
Sbjct: 61  MTLEQRTAILHKVADGINARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADMIKN 120

Query: 121 VANEAFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPS 180
           V  E+FEM TPDG GA+NYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPS
Sbjct: 121 VPTESFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPS 180

Query: 181 EETPLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVI 240
           EETP T  LLGEVM+ AGVP GVYNVVHGFGGDSAGA+LTEHP VD +TFTGETGTGEVI
Sbjct: 181 EETPTTTALLGEVMKEAGVPDGVYNVVHGFGGDSAGAYLTEHPQVDGFTFTGETGTGEVI 240

Query: 241 MRAAAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPI 300
           M+AAAKG+R +SLELGGKNAG+VFADCDM+KAIEGT+RSAFANCGQVCLGTERVYVER I
Sbjct: 241 MKAAAKGIRDISLELGGKNAGLVFADCDMEKAIEGTMRSAFANCGQVCLGTERVYVERSI 300

Query: 301 FDEFVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVP 360
           FDEFV RLK  AE L IGPPDDA +N GPLVSLKHREKVLSYYQ+AVDDG +V+TGGGVP
Sbjct: 301 FDEFVGRLKEAAEGLKIGPPDDADANLGPLVSLKHREKVLSYYQKAVDDGATVVTGGGVP 360

Query: 361 DMPAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLAS 420
           DMPA LAGGAWV+PTIWTGL DDSAVVT+EIFGPCCHIRPFDTEEEAIELANSLPYGLAS
Sbjct: 361 DMPAELAGGAWVEPTIWTGLPDDSAVVTDEIFGPCCHIRPFDTEEEAIELANSLPYGLAS 420

Query: 421 AIWTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELK 480
           AIW+EN +RAHRVAGQIEAGI+WVNSWFLRDLRT FGGSKQSG+GREGGVHSLEFYTE+K
Sbjct: 421 AIWSENITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGVGREGGVHSLEFYTEMK 480

Query: 481 NICVKL 486
           NICVKL
Sbjct: 481 NICVKL 486


Lambda     K      H
   0.318    0.136    0.411 

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: 936
Number of extensions: 22
Number of successful extensions: 1
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: 486
Length of database: 486
Length adjustment: 34
Effective length of query: 452
Effective length of database: 452
Effective search space:   204304
Effective search space used:   204304
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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