GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Klebsiella michiganensis M5al

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BWI76_RS11680 BWI76_RS11680 succinylglutamate-semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS11680 BWI76_RS11680
           succinylglutamate-semialdehyde dehydrogenase
          Length = 492

 Score =  784 bits (2024), Expect = 0.0
 Identities = 384/489 (78%), Positives = 424/489 (86%)

Query: 1   MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE 60
           M+LWINGDW +G+G +R K NPVS  +LWQGNDADA QV  A  AARAAFP WAR  FA 
Sbjct: 1   MSLWINGDWQSGRGPARSKHNPVSQTLLWQGNDADADQVALAVSAARAAFPAWARQPFAA 60

Query: 61  RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR 120
           R A+ E+FA+LLE+NK+ELTA+IARETGKPRWEAATE+TAMINKIAIS+ AYH RTGE +
Sbjct: 61  RKAIAEKFASLLEANKSELTAVIARETGKPRWEAATEITAMINKIAISVNAYHSRTGEAQ 120

Query: 121 SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV 180
           + M DG A+LRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNT++FKPSELTP SGEAV
Sbjct: 121 TAMADGEATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPQSGEAV 180

Query: 181 MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240
           ++LW +AGLPPGVLNL+QGGRETG+ALS   D+DGLLFTGS+ TG+QLHRQL+GQPEKIL
Sbjct: 181 VKLWAEAGLPPGVLNLLQGGRETGEALSGQADIDGLLFTGSSATGFQLHRQLAGQPEKIL 240

Query: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300
           ALEMGGNNPLI+D+  DIDAAVHLTIQSAF+TAGQRCTCARRLL+K G  GDAFL RLV 
Sbjct: 241 ALEMGGNNPLIVDDPQDIDAAVHLTIQSAFITAGQRCTCARRLLVKRGEAGDAFLQRLVT 300

Query: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360
           VSQ L P  WD EPQPFIGGLIS QAAQ+V  AW    A GG+ LL PRLLQAGTSLLTP
Sbjct: 301 VSQTLIPAAWDAEPQPFIGGLISAQAAQKVHQAWLAHVASGGKTLLEPRLLQAGTSLLTP 360

Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420
           GIIEM+ VA V DEEVFGPLL VWRYD FDEAI +AN TRFGLSCGL+S ER+KFDQLLL
Sbjct: 361 GIIEMSAVAQVADEEVFGPLLCVWRYDHFDEAIALANATRFGLSCGLISAERDKFDQLLL 420

Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480
           EARAGIVNWNKPLTGAASTAPFGG GASGNHRP AWYAADYCAWPMASLES  L+LPATL
Sbjct: 421 EARAGIVNWNKPLTGAASTAPFGGTGASGNHRPGAWYAADYCAWPMASLESPELSLPATL 480

Query: 481 NPGLDFSDE 489
           +PGL+F  E
Sbjct: 481 SPGLNFRQE 489


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: 949
Number of extensions: 38
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: 492
Length adjustment: 34
Effective length of query: 458
Effective length of database: 458
Effective search space:   209764
Effective search space used:   209764
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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