GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Escherichia coli BW25113

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 15507 b1385 phenylacetaldehyde dehydrogenase (VIMSS)

Query= reanno::pseudo5_N2C3_1:AO356_23175
         (500 letters)



>lcl|FitnessBrowser__Keio:15507 b1385 phenylacetaldehyde
           dehydrogenase (VIMSS)
          Length = 499

 Score =  240 bits (612), Expect = 1e-67
 Identities = 167/486 (34%), Positives = 253/486 (52%), Gaps = 16/486 (3%)

Query: 8   GHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPA--WSEQSS 65
           G YIDGR   + + +   +F+PATG   A  A A  + VD AV SA  AF +  W+ +  
Sbjct: 21  GLYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMSAWRAFVSRRWAGRLP 80

Query: 66  LRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHG-EVTRGIEIVEYACGAPNLL-- 122
             R R++ +F +L+++H +ELAQ+ + E GK ++ +   EV   +  + Y  G    +  
Sbjct: 81  AERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGLTTKIAG 140

Query: 123 KT-DFSDNI--GGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSE 179
           KT D S  +  G     W  ++P+GV AG+ P+NFP+M+ +W +  AL AG   ++KPSE
Sbjct: 141 KTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIVIKPSE 200

Query: 180 RDPSASLLMARLLTEAGLPDGVFNVVQGD-KVAVDALLQHPDIEAISFVGSTPIAEYIHQ 238
             P   L +A L +EAG+PDGVFNVV G   V   AL  HP +  ISF GST   + I +
Sbjct: 201 TTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVAKISFTGSTATGKGIAR 260

Query: 239 QGTAQGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGD 298
                  RV    G KN  IV+ DAD     + L+  ++ + G+ C A S       + D
Sbjct: 261 TAADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIEAPLFD 320

Query: 299 ELIAKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKV 358
            L++     +  L++G G  P   + PLV+  H  KV  F+D   A+ A LI   RG   
Sbjct: 321 TLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQQAELI---RGSNG 377

Query: 359 PGAEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCF 418
           P  E G++V  TL     A++ + ++E+FGPV+ +VRV D   A+ L N  E+G   S +
Sbjct: 378 PAGE-GYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGLTASVW 436

Query: 419 TRDGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYK 478
           T++   A  ++  ++ G V +N    +  A   FGG K+S  G    +G + L  +   K
Sbjct: 437 TQNLSQALEYSDRLQAGTVWVNSHTLID-ANLPFGGMKQS--GTGRDFGPDWLDGWCETK 493

Query: 479 SVMQRW 484
           SV  R+
Sbjct: 494 SVCVRY 499


Lambda     K      H
   0.320    0.137    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: 559
Number of extensions: 22
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: 500
Length of database: 499
Length adjustment: 34
Effective length of query: 466
Effective length of database: 465
Effective search space:   216690
Effective search space used:   216690
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 (21.8 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, 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