GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Marinobacter adhaerens HP15

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase

Query= metacyc::MONOMER-16244
         (495 letters)



>FitnessBrowser__Marino:GFF3684
          Length = 489

 Score =  348 bits (893), Expect = e-100
 Identities = 194/476 (40%), Positives = 278/476 (58%), Gaps = 10/476 (2%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           F++  F+ + + +TF  V+P+T + I +V  A       A+E+A A F + WS      R
Sbjct: 11  FVHGRFLANSTGETFPVVNPATGQVIYEVEVADESVQQAAIESARAGF-AEWSAMTAIER 69

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSVI 142
            ++L +   ++ E  D LA  E  D GK    ++  DV   A      AG    I+G+  
Sbjct: 70  SRILLRAVAILRERNDELAAAEVRDTGKPWQEAEAVDVVTGADAVEFFAGLAPSIEGNQQ 129

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           + G   F YTRREP+G+C  I  WN+P+ +A WK  P L  G   + K +E TP+ A+ L
Sbjct: 130 DLGGD-FYYTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPSEETPMGAVKL 188

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
           A +  EAG P GV NVV G     G  ++ HP+I KV+FTG  ATG+ +M AAA S LK 
Sbjct: 189 AEIFTEAGVPAGVFNVVQG-AAEVGQWLTHHPEIAKVSFTGEVATGKKVM-AAASSTLKD 246

Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF-K 321
           VT+ELGGKSP I+FDDAD+++ I   + G FY  GE+C  G+R++V E +Y + +    +
Sbjct: 247 VTMELGGKSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFIERLLE 306

Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERF----GNKGY 377
               ++K GDP   DT  GA  S    D +L YI  G  EGAT+  GG  F       GY
Sbjct: 307 RTRNNIKPGDPMNPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDSKGGY 366

Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437
           F++PTIF D  +D  IV++EIFGPV+++  F+  +EVIA AN+++ GLAAGV T ++  A
Sbjct: 367 FVEPTIFTDCTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAGVFTNDIRRA 426

Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493
             V ++I +G  W+N+Y      +P GGY  SGIGRE G E + +YTQ+K+V +G+
Sbjct: 427 HRVIHQIQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYVGM 482


Lambda     K      H
   0.316    0.133    0.389 

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: 598
Number of extensions: 34
Number of successful extensions: 7
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: 495
Length of database: 489
Length adjustment: 34
Effective length of query: 461
Effective length of database: 455
Effective search space:   209755
Effective search space used:   209755
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 (21.6 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