GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Escherichia coli BW25113

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 15507 b1385 phenylacetaldehyde dehydrogenase (VIMSS)

Query= reanno::SB2B:6938906
         (486 letters)



>FitnessBrowser__Keio:15507
          Length = 499

 Score =  181 bits (459), Expect = 5e-50
 Identities = 146/453 (32%), Positives = 223/453 (49%), Gaps = 23/453 (5%)

Query: 15  KEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDA--QFEWFMLGFEGRQAIVEAYRNEL 72
           K +   +PA G+ I     A  A V  AVM+A  A     W       R+ I+  + + +
Sbjct: 35  KRLAIFDPATGQEIASTADANEADVDNAVMSAWRAFVSRRWAGRLPAERERILLRFADLV 94

Query: 73  EANKAELAEVIAQETGKP-----RWETATEAAAMIGKIGLSVSAYHKRTGTEVN--EGAA 125
           E +  ELA++   E GK       +E       M    GL+     K     +   +GA 
Sbjct: 95  EQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGLTTKIAGKTLDLSIPLPQGAR 154

Query: 126 GRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELMLKLWE 185
            +A  R +P GVVA   P+NFP  +    ++PAL AG ++V KPSE TP     + +L  
Sbjct: 155 YQAWTRKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIVIKPSETTPLTMLRVAELAS 214

Query: 186 KAGLPAGVINLVQGE-VETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKILALEM 244
           +AG+P GV N+V G     G AL SHP +  + FTGS+ TG  + +  A H  ++  LE+
Sbjct: 215 EAGIPDGVFNVVTGSGAVCGAALTSHPHVAKISFTGSTATGKGIARTAADHLTRV-TLEL 273

Query: 245 GGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVEAVKA 304
           GG NP IV   +D +  I  ++  +F++ GQ C  + R+Y+E     D L++G  +AVK+
Sbjct: 274 GGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIE-APLFDTLVSGFEQAVKS 332

Query: 305 IKVGPWN---ADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTG-LVSP 360
           ++VGP     A   P +     +     + DAQ          L+  ++  AG G  V+P
Sbjct: 333 LQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQ-----QAELIRGSNGPAGEGYYVAP 387

Query: 361 GL-IDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFL 419
            L ++    + L  EE FGP++ +VR    +EA++LANDT YGL+A +   + +    + 
Sbjct: 388 TLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGLTASVWTQNLSQALEYS 447

Query: 420 ARIRAGIVNWNKQITGASGAAPFGGVGASGNHR 452
            R++AG V W    T      PFGG+  SG  R
Sbjct: 448 DRLQAGTV-WVNSHTLIDANLPFGGMKQSGTGR 479


Lambda     K      H
   0.317    0.133    0.393 

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: 581
Number of extensions: 28
Number of successful extensions: 5
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: 486
Length of database: 499
Length adjustment: 34
Effective length of query: 452
Effective length of database: 465
Effective search space:   210180
Effective search space used:   210180
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:

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