GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Marinobacter adhaerens HP15

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I

Query= SwissProt::Q9I6M5
         (483 letters)



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

 Score =  653 bits (1684), Expect = 0.0
 Identities = 311/486 (63%), Positives = 392/486 (80%), Gaps = 3/486 (0%)

Query: 1   MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60
           ++LK+ +L R+QAY++G W+ A +G+T  VN+PA GE + +VP M   + R AIEAA  A
Sbjct: 3   LELKNRELLREQAYINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAA 62

Query: 61  LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120
            PAWR+  AKERAN LR+WF+L++ NQ+DLARLMT EQGKPLAE++GE+ Y ASF+EWF 
Sbjct: 63  WPAWRSTPAKERANILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFA 122

Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180
           EEAKR YGD IPGH  DKRI+VIKQP+GV AAITPWNFP AMITRK  PALAAGC +V+K
Sbjct: 123 EEAKRAYGDVIPGHGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVK 182

Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGS---AGEVGGELTSNPIVRKLTFTGSTEI 237
           PA  TP SALA+  LAE AG+P G+ +++T S   A  VG ELT NPIVRK++FTGST +
Sbjct: 183 PAEDTPLSALAITALAEEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPV 242

Query: 238 GRQLMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYV 297
           G+ LM + +  +KKVSLELGGNAPFIVFDDADLDAAV G + SKYRN GQTCVCANR+YV
Sbjct: 243 GKLLMRQASDTVKKVSLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYV 302

Query: 298 QDGVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSG 357
           Q GVYDAF +KLKAAV+K+ +G GLE     GPLI+  A+AKV+ HI DA SKGAKV  G
Sbjct: 303 QAGVYDAFAEKLKAAVSKMVVGPGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALG 362

Query: 358 GKPHALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASY 417
           G+ H+LGGTFFEPTIL    +  L++++ETFGP+AP+F+F+ + E IAM+ND+EFGL++Y
Sbjct: 363 GRAHSLGGTFFEPTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAY 422

Query: 418 FYARDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY 477
           FY+R++ RV+RVAE+LE GM+G+N G+IS EVAPFGG+K SGLGREGS YG+++Y+E+KY
Sbjct: 423 FYSRNIHRVWRVAEELESGMIGVNEGIISTEVAPFGGVKESGLGREGSHYGLDEYMELKY 482

Query: 478 LCLGGI 483
           LCLGG+
Sbjct: 483 LCLGGM 488


Lambda     K      H
   0.317    0.135    0.391 

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: 727
Number of extensions: 10
Number of successful extensions: 2
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: 483
Length of database: 489
Length adjustment: 34
Effective length of query: 449
Effective length of database: 455
Effective search space:   204295
Effective search space used:   204295
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