GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Klebsiella michiganensis M5al

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate BWI76_RS05685 BWI76_RS05685 dihydrodipicolinate synthase family protein

Query= BRENDA::A9CL97
         (313 letters)



>FitnessBrowser__Koxy:BWI76_RS05685
          Length = 309

 Score =  414 bits (1063), Expect = e-120
 Identities = 202/305 (66%), Positives = 246/305 (80%)

Query: 1   MDLRGLSPAPVTAFTRDGEVDYAANAKIARWLASMEGVKSLVILGHAGEGTFLTEDERLE 60
           +DLRGL+PAPVT FTRDG VDY A  ++  WL S++GVK LV+LGHAGEGTFLT++E+  
Sbjct: 4   IDLRGLTPAPVTPFTRDGRVDYDAIQRLGNWLGSIDGVKGLVVLGHAGEGTFLTQEEQAN 63

Query: 61  LIRVYVDAVGGSLPIIAGITGEGTRVAAAEAKKCKAAGATGALVYPNHGWLRFGFQRGAP 120
           +IR +V +V   LPIIAGITGEGT VAA EAK+  AAGA+  L+YP+HGWLRFG+Q GAP
Sbjct: 64  VIRAFVKSVDDKLPIIAGITGEGTEVAALEAKRAVAAGASAGLLYPSHGWLRFGYQDGAP 123

Query: 121 QDRYKAIWEESGLQEILFQYPDVTKASYDLDTQLAIATQPGVVATKNGVRNMKRWYVEIP 180
           QDRY+ ++EESGL  ILFQYPDVTKA+Y+L T L I+ QPGV A KNGVRNM+RW  EIP
Sbjct: 124 QDRYRVVYEESGLPLILFQYPDVTKATYNLKTLLDISAQPGVFAMKNGVRNMRRWDTEIP 183

Query: 181 ELKNANPNLQVLSCHDEWLLPTMFDVDGLLVGYGNIAPELLIDLIKAGKAQDYPQARKIF 240
            ++   P+LQ+LSCHDE+LL T FDVDG LVGYGNIAPE LI++IKAGKA DY +AR++ 
Sbjct: 184 VIRRERPDLQILSCHDEYLLHTAFDVDGFLVGYGNIAPEPLIEMIKAGKAGDYVKARQLH 243

Query: 241 EQLLPVTRAVYHRGSHMEGTVALKLGLVHRGVLDHATIREPLKNLGEKAEQEIFAAFDAA 300
           ++LLPVT++VYHRGSHMEGTVALK  LV RG+L+HAT+R PL  L   AE+EI  A  AA
Sbjct: 244 DRLLPVTKSVYHRGSHMEGTVALKHALVARGILEHATVRSPLLPLENGAEKEIHDAMRAA 303

Query: 301 GIGRV 305
            +GRV
Sbjct: 304 ELGRV 308


Lambda     K      H
   0.319    0.137    0.405 

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: 340
Number of extensions: 7
Number of successful extensions: 1
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: 313
Length of database: 309
Length adjustment: 27
Effective length of query: 286
Effective length of database: 282
Effective search space:    80652
Effective search space used:    80652
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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