GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Methylocystis bryophila S285

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  375 bits (964), Expect = e-108
 Identities = 214/488 (43%), Positives = 293/488 (60%), Gaps = 20/488 (4%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           FI  +W   +  + F  ++P TG  ICQVA G   DV+ A+ AA  A      W +  A+
Sbjct: 22  FIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKA---KDAWGKTPAA 78

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R  +LN++A  ++ + + LA +ET+DNGKP   +   D+ + +   RY+AG      G 
Sbjct: 79  ERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQEGS 138

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
              ID D  +Y  HEP+GV GQIIPWNFP+LM AWKL PALA GN VV+K AEQTP++ L
Sbjct: 139 LSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPMSIL 198

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            VA LI +   PPGV+NIV GFG  AG  +AS++ + K+AFTG T  GR+I   A + NL
Sbjct: 199 AVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYA-AENL 256

Query: 280 KRVTLELGGKSPNIIMS------DADMDWAVEQ-AHFALFFNQGQCCCAGSRTFVQEDIY 332
             VTLELGGKSPNI  +      DA +D A+E  A FAL  NQG+ C   SR  VQ  IY
Sbjct: 257 IPVTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFAL--NQGEVCTCPSRALVQRSIY 314

Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAA 392
           D+F+E+++AR      G+P D  T  G Q    Q +KIL Y++ G++EGAK+L GG  + 
Sbjct: 315 DKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERSV 374

Query: 393 -----DRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447
                  GY++QPT   +  + M + +EEIFGPV+ +  F+T EE +  AN++ YGL A 
Sbjct: 375 LEGELKEGYYMQPTAL-EGHNRMRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAG 433

Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 507
           ++T+D  +A    +A++AG VW NCY  + A + FGGYK SG GRE  +  L  Y + K 
Sbjct: 434 LWTRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKN 493

Query: 508 VTVKVPQK 515
           + V    K
Sbjct: 494 LLVSYSPK 501


Lambda     K      H
   0.319    0.136    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: 583
Number of extensions: 29
Number of successful extensions: 6
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: 517
Length of database: 506
Length adjustment: 35
Effective length of query: 482
Effective length of database: 471
Effective search space:   227022
Effective search space used:   227022
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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