GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxD in Escherichia coli BW25113

Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate 15509 b1387 fused aldehyde dehydrogenase/enoyl-CoA hydratase (NCBI)

Query= BRENDA::Q13WK4
         (531 letters)



>FitnessBrowser__Keio:15509
          Length = 681

 Score =  408 bits (1048), Expect = e-118
 Identities = 229/524 (43%), Positives = 321/524 (61%), Gaps = 20/524 (3%)

Query: 5   LKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYAQ 64
           L + ++G W +G G    +   ++G AL  V+SEGLD+A A  FA E G  ALRA+T+ +
Sbjct: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63

Query: 65  RAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEVH 123
           RAA L  + K L +++  +YA++ A +G TR DS VDI+GGI TL  YA LG+  L +  
Sbjct: 64  RAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDT 122

Query: 124 ALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183
              +     LSK+  F+A+H+L+   GVA+ INAFNFP WG+ EK AP  L G+P I+KP
Sbjct: 123 LWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKP 182

Query: 184 ATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLRA 243
           ATATA LTQ MV  +VD+G++P GA+S+ICGS+  LLD + S DVV+FTGSA T   LR 
Sbjct: 183 ATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRV 242

Query: 244 HPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303
            P  V +     +EADSLN  +L  D TPD P F LFI+EVVREMT K+GQKCTAIRR  
Sbjct: 243 QPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRII 302

Query: 304 VPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAYD 363
           VP+A +  V +AL A+L K+ VG+P  + V+MG+LV+ EQ  +V       +E+  +   
Sbjct: 303 VPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADV-------QEKVNILLA 355

Query: 364 SSAVPLIDADANIAACVA---PHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNAL 420
           +     +   A+++A  A   P L     PD    +H  E FGPVA++ P        A 
Sbjct: 356 AGCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMP--------AQ 407

Query: 421 PEAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVM 480
            + HA+ LA  G GSL  ++ + D     +   + A +HGR+  ++       TGHG+ +
Sbjct: 408 NQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPL 467

Query: 481 PMSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLTQ 524
           P  +HGGPGRAGGGEELGGLRA+  Y +R+A+Q +   +  +++
Sbjct: 468 PQLVHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISK 511


Lambda     K      H
   0.318    0.132    0.379 

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: 759
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: 531
Length of database: 681
Length adjustment: 37
Effective length of query: 494
Effective length of database: 644
Effective search space:   318136
Effective search space used:   318136
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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