GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Marinobacter adhaerens HP15

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__Marino:GFF964
          Length = 505

 Score =  392 bits (1006), Expect = e-113
 Identities = 208/470 (44%), Positives = 296/470 (62%), Gaps = 4/470 (0%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           ++N  +  A + + F +V+P  G  +  +A  D+ D D+AV AARAAF+ G  W ++  +
Sbjct: 30  YLNGTYQWAANGEAFTSVSPIDGRELASIASCDQSDADQAVMAARAAFEAGI-WSQLAPA 88

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R  +L R A+LIE     LA LETLD GKP   +  VD+    + +R+ A   DK +G+
Sbjct: 89  KRKAVLLRFAELIEAHGDELALLETLDMGKPINHASNVDVPATARAIRWTAEAIDKVYGE 148

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
             P   +       EP+GV   I+PWNFP++M AWK+ PALATGN V++K +E++PL+A+
Sbjct: 149 LAPTPHNQIGMISREPMGVVAAIVPWNFPMIMAAWKIAPALATGNSVILKPSEKSPLSAI 208

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            +A L  EAG P GV N++PG+G T G A+A H DVD + FTGST + + + + AG SN+
Sbjct: 209 RLAALAGEAGVPAGVFNVLPGYGHTVGKALALHMDVDCLVFTGSTNVAKQLMIYAGQSNM 268

Query: 280 KRVTLELGGKSPNIIMSDA-DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338
           KRV LE GGKSPNI+ +DA D+  A  +A  A+ FNQG+ C AGSR  V+  I  EFV  
Sbjct: 269 KRVWLEAGGKSPNIVFADAPDLKKAAAEAASAIAFNQGEVCTAGSRLLVENSIRAEFVRL 328

Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADR--GY 396
                K+   G+P D  T  G  VD+ Q  +I+ YI  G+ EGA+L+ GG    +   G 
Sbjct: 329 ICEALKTWRPGHPLDPATTCGAIVDQAQLDRIIDYIGIGQSEGARLVEGGQRILENTGGL 388

Query: 397 FIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKA 456
           F+QPTVF  V + M IA EEIFGPV+ ++ F T +E V  AN+S YGLAAAV+T +++ A
Sbjct: 389 FVQPTVFDGVNNQMRIASEEIFGPVLSVIGFDTADEAVAIANDSIYGLAAAVWTSNINTA 448

Query: 457 NYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVK 506
           + +++AL+AG+VW+N YD     +PFGG+K SG+GR+   +    YTE+K
Sbjct: 449 HKVAKALRAGSVWINHYDGGDMTAPFGGFKQSGNGRDKSVHAFDKYTELK 498


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: 627
Number of extensions: 26
Number of successful extensions: 4
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: 505
Length adjustment: 35
Effective length of query: 482
Effective length of database: 470
Effective search space:   226540
Effective search space used:   226540
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