GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kauB in Escherichia coli BW25113

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 15420 b1300 gamma-Glu-gamma-aminobutyraldehyde dehydrogenase, NAD(P)H-dependent (NCBI)

Query= metacyc::MONOMER-11560
         (497 letters)



>lcl|FitnessBrowser__Keio:15420 b1300
           gamma-Glu-gamma-aminobutyraldehyde dehydrogenase,
           NAD(P)H-dependent (NCBI)
          Length = 495

 Score =  570 bits (1469), Expect = e-167
 Identities = 288/491 (58%), Positives = 354/491 (72%), Gaps = 4/491 (0%)

Query: 7   ADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENA 66
           A W+ +A  L IE R FINGEYT A   ETFE + PV    LAK+A     D +RA+  A
Sbjct: 7   AYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAA 66

Query: 67  RATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQ 126
           R  F  G WS  +PAKRKA L + ADL+  + EELALLETLD GKPI  S   DIPGAA+
Sbjct: 67  RGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAAR 126

Query: 127 AIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGN 186
           AI W AEAIDKVY EVA T   +L ++ REPVGV+ AIVPWNFPLL+ CWKLGPALA GN
Sbjct: 127 AIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGN 186

Query: 187 SVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGST 246
           SV+LKPSEKSPL+AIR+A LA EAG+P GVLNV+ G+GH  G+AL+ H D+D + FTGST
Sbjct: 187 SVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGST 246

Query: 247 KIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGS 306
           +  KQL+  AG+SNMKR+WLEAGGKS NIVFAD PDLQ AA A A+ I +NQG+VC AG+
Sbjct: 247 RTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGT 306

Query: 307 RLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAK 366
           RLL+E SI D+FL ++ +  + W+PG+PLDP TT+G L+D    ++V S+I  G   G  
Sbjct: 307 RLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQL 366

Query: 367 LLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTP 426
           LL G    L    G    PTIF  V     +++EEIFGPVL V  F + E+A+ +AND+ 
Sbjct: 367 LLDGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQ 422

Query: 427 YGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEK 486
           YGL A +WT D+S+AH+ +R ++AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHALEK
Sbjct: 423 YGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEK 482

Query: 487 YTELKATWIKL 497
           +TELK  WI L
Sbjct: 483 FTELKTIWISL 493


Lambda     K      H
   0.316    0.132    0.390 

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: 663
Number of extensions: 18
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: 497
Length of database: 495
Length adjustment: 34
Effective length of query: 463
Effective length of database: 461
Effective search space:   213443
Effective search space used:   213443
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 (21.6 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