GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Escherichia coli BW25113

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 15507 b1385 phenylacetaldehyde dehydrogenase (VIMSS)

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__Keio:15507
          Length = 499

 Score =  323 bits (827), Expect = 1e-92
 Identities = 186/485 (38%), Positives = 276/485 (56%), Gaps = 16/485 (3%)

Query: 2   QHKLLINGELVSGEGEKQ-PVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQT 58
           QH L I+G     + EK+  +++PATG  +   A+A+   VD AV +A  AF    W   
Sbjct: 19  QHGLYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMSAWRAFVSRRWAGR 78

Query: 59  TPKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCL 118
            P  R   LL+ AD++E++ +  A+LE+   GK +  +   E+   ++  R+ AG    +
Sbjct: 79  LPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGLTTKI 138

Query: 119 NG--------LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVV 170
            G        L  G   +  T   R++P+GVVA I PWN+PLM+  WK+ PALAAG  +V
Sbjct: 139 AGKTLDLSIPLPQGARYQAWT---RKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIV 195

Query: 171 LKPSEITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATG 229
           +KPSE TPLT L++AELA +   P GV N++ G G   G  LT HP V  +S TGS ATG
Sbjct: 196 IKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVAKISFTGSTATG 255

Query: 230 EHIISHTASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQ 289
           + I    A  + R  +ELGGK P IV  DAD + V+EG+ T  + N GQ C A+ RIY +
Sbjct: 256 KGIARTAADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIE 315

Query: 290 KGIYDTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITG 349
             ++DTLV     AV +L+ G       ++ PL S AH ++V   +++A+A    ++I G
Sbjct: 316 APLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQ-QAELIRG 374

Query: 350 GEKRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASS 409
                G GYY APTL+        + ++EVFGPVV++    + E+ +  AND++YGL +S
Sbjct: 375 SNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGLTAS 434

Query: 410 VWTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRH 469
           VWT+++ +A   S RLQ G  WVN+H ++ + +P GG K SG G+D     L+ +   + 
Sbjct: 435 VWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPDWLDGWCETKS 494

Query: 470 VMVKH 474
           V V++
Sbjct: 495 VCVRY 499


Lambda     K      H
   0.317    0.134    0.397 

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: 568
Number of extensions: 27
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: 474
Length of database: 499
Length adjustment: 34
Effective length of query: 440
Effective length of database: 465
Effective search space:   204600
Effective search space used:   204600
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 (21.7 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