GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6937470
          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:

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