GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Marinobacter adhaerens HP15

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I

Query= BRENDA::P25553
         (479 letters)



>lcl|FitnessBrowser__Marino:GFF2064 HP15_2020 succinate-semialdehyde
           dehydrogenase I
          Length = 489

 Score =  340 bits (873), Expect = 5e-98
 Identities = 185/471 (39%), Positives = 277/471 (58%), Gaps = 4/471 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           YI+GQ++T +      V +PA    ++ +PD    DAR AI+AA  A P W + PA ERA
Sbjct: 16  YINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAAWPAWRSTPAKERA 75

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           + LRK    +     +++ L+  E GK    +  EV + A +I++ AE A+R  G++I  
Sbjct: 76  NILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFAEEAKRAYGDVIPG 135

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
               + I++ K+ +GV   I PWNFP  +I RK+APAL  G  +V+KP+E TP +A+A  
Sbjct: 136 HGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVKPAEDTPLSALAIT 195

Query: 190 KIVDEIGLPRGVFNLVL---GRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNIT 246
            + +E G+P G+ N++        +VG EL GNP V  VS TGS   G+ +M  A+  + 
Sbjct: 196 ALAEEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPVGKLLMRQASDTVK 255

Query: 247 KVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLG 306
           KV LELGG AP IV DDADL+ AV  ++ S+  N+GQ C CA RVYVQ G+YD F  +L 
Sbjct: 256 KVSLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYVQAGVYDAFAEKLK 315

Query: 307 EAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYP 366
            A+  +  G P    +   GPLIN AAL +V++ +  A  +GA+VA GG+A    G ++ 
Sbjct: 316 AAVSKMVVG-PGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALGGRAHSLGGTFFE 374

Query: 367 PTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKA 426
           PT+L    QEM I  EETFGPV P+  F+T ++AI+MANDS++GL++  Y++N++   + 
Sbjct: 375 PTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAYFYSRNIHRVWRV 434

Query: 427 IKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
            + L+ G   +N            G ++SG+G     +GL EY++ + + L
Sbjct: 435 AEELESGMIGVNEGIISTEVAPFGGVKESGLGREGSHYGLDEYMELKYLCL 485


Lambda     K      H
   0.318    0.135    0.392 

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: 585
Number of extensions: 34
Number of successful extensions: 3
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: 479
Length of database: 489
Length adjustment: 34
Effective length of query: 445
Effective length of database: 455
Effective search space:   202475
Effective search space used:   202475
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