GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Shewanella amazonensis SB2B

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 6937470 Sama_1626 succinylglutamic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P76217
         (492 letters)



>lcl|FitnessBrowser__SB2B:6937470 Sama_1626 succinylglutamic
           semialdehyde dehydrogenase (RefSeq)
          Length = 495

 Score =  554 bits (1427), Expect = e-162
 Identities = 272/481 (56%), Positives = 351/481 (72%)

Query: 4   WINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHA 63
           +I G W  G G      NP +GEV+W GN A+A QV+ A +AAR+AF  W+ +  AER A
Sbjct: 13  FIGGQWQPGHGKGFESINPANGEVIWCGNGANAEQVDTAVKAARSAFYNWSAMPLAERLA 72

Query: 64  VVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEM 123
           ++E F A L  +   +  +IA ETGK  WE+ TEV AM  KIAISI+A+  RTG   + M
Sbjct: 73  IIEAFGAQLGEHSEAMARLIAEETGKALWESRTEVAAMTGKIAISIRAHSERTGTVENPM 132

Query: 124 PDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRL 183
           P   A +RH+PHGV+AVFGPYNFPGHLPNGHIVPAL+AGNT++FKPSELTP   +  + L
Sbjct: 133 PGARAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAQFTVEL 192

Query: 184 WQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALE 243
           WQ+AGLP GV+NL+QG  ETG+AL+    +DGL FTGS+NTG+ LH+Q +GQP KILALE
Sbjct: 193 WQKAGLPAGVINLLQGEVETGKALAGHPGIDGLFFTGSSNTGHLLHQQYAGQPGKILALE 252

Query: 244 MGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQ 303
           MGGNNPLI+ +VA+++AAVH  IQSAF+++GQRCTCARRL +K  A GDA LA+L+  S+
Sbjct: 253 MGGNNPLIVKDVANVNAAVHDIIQSAFISSGQRCTCARRLFIKKDANGDAILAKLIEASR 312

Query: 304 RLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGII 363
           ++       E QPF G +IS +AA  +V A   ++++GG  LL  +        +TPGII
Sbjct: 313 QIRVDEPFAENQPFYGAMISAKAAAAMVKAQTDIQSLGGISLLELKQPDLALGFVTPGII 372

Query: 364 EMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEAR 423
           ++T V  +PDEE FGPLL+V+RYD FD AI  ANNT FGLS GL++     +D      R
Sbjct: 373 DVTHVKALPDEEHFGPLLKVYRYDDFDAAIDEANNTAFGLSAGLLADNEADYDHFFRRIR 432

Query: 424 AGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLNPG 483
           AGIVNWNKP+TGA+S APFGGIGASGNHR SA+YAADYCA+P++S+E+ S++LPA+L+PG
Sbjct: 433 AGIVNWNKPITGASSAAPFGGIGASGNHRASAFYAADYCAYPVSSVEASSVSLPASLSPG 492

Query: 484 L 484
           L
Sbjct: 493 L 493


Lambda     K      H
   0.318    0.134    0.412 

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: 810
Number of extensions: 33
Number of successful extensions: 1
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: 492
Length of database: 495
Length adjustment: 34
Effective length of query: 458
Effective length of database: 461
Effective search space:   211138
Effective search space used:   211138
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 (21.7 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 paper from 2022 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