Alignments for a candidate for praB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for praB in Marinobacter adhaerens HP15

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF1133 HP15_1111 betaine aldehyde dehydrogenase

Query= BRENDA::Q1XGK8
         (486 letters)



>FitnessBrowser__Marino:GFF1133
          Length = 493

 Score =  850 bits (2195), Expect = 0.0
 Identities = 405/486 (83%), Positives = 444/486 (91%)

Query: 1   MKEIKHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGK 60
           MKEIKH ING +V S S R F+++NP+NG++I  VHEAGR EVDAAVKAARAAL+GPWGK
Sbjct: 8   MKEIKHHINGQYVSSCSSRLFDNVNPANGKIISKVHEAGREEVDAAVKAARAALRGPWGK 67

Query: 61  LSVAERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKN 120
           +++ ER  ILH+VADGI ARFDEFLE ECLDTGKPKS+ASHIDIPRGAANFKVFAD++KN
Sbjct: 68  MTLDERTSILHKVADGINARFDEFLEGECLDTGKPKSMASHIDIPRGAANFKVFADMIKN 127

Query: 121 VANEAFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPS 180
           V  E+FEM TPDG GA+NYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPS
Sbjct: 128 VPTESFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPS 187

Query: 181 EETPLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVI 240
           EETP T TLLGEVM+ AGVP GV+NVVHGFGGDSAGAFLTEHP VD  TFTGE GTGEVI
Sbjct: 188 EETPTTTTLLGEVMKEAGVPDGVFNVVHGFGGDSAGAFLTEHPQVDGITFTGEIGTGEVI 247

Query: 241 MRAAAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPI 300
           M+AAAKG+R +SLELGGKNAG+VFADCD+DKAIEGT+RSAFANCGQVCLGTERVYVER I
Sbjct: 248 MKAAAKGIRDISLELGGKNAGVVFADCDIDKAIEGTMRSAFANCGQVCLGTERVYVERSI 307

Query: 301 FDEFVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVP 360
           FDEFV RLK  AE + IGPPDDA ++ GPLVSL HREKVLSYYQ+AVDDG +V+TGGGVP
Sbjct: 308 FDEFVGRLKEAAEGMKIGPPDDAEADMGPLVSLNHREKVLSYYQKAVDDGATVVTGGGVP 367

Query: 361 DMPAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLAS 420
           +MP  LAGGAWVQPTIWTGL +DSAV+T+EIFGPCCHIRPFDTEEEAIELANSLPYGLAS
Sbjct: 368 EMPEALAGGAWVQPTIWTGLPEDSAVITDEIFGPCCHIRPFDTEEEAIELANSLPYGLAS 427

Query: 421 AIWTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELK 480
           AIW+EN +RAHRVAGQIEAGI+WVNSWFLRDLRT FGGSKQSGIGREGGVHSLEFYTE+K
Sbjct: 428 AIWSENITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGIGREGGVHSLEFYTEMK 487

Query: 481 NICVKL 486
           NICVKL
Sbjct: 488 NICVKL 493


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: 913
Number of extensions: 21
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: 493
Length adjustment: 34
Effective length of query: 452
Effective length of database: 459
Effective search space:   207468
Effective search space used:   207468
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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