GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Klebsiella michiganensis M5al

Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate BWI76_RS04670 BWI76_RS04670 3-isopropylmalate dehydratase large subunit

Query= BRENDA::Q58409
         (420 letters)



>FitnessBrowser__Koxy:BWI76_RS04670
          Length = 466

 Score =  237 bits (604), Expect = 6e-67
 Identities = 156/462 (33%), Positives = 236/462 (51%), Gaps = 50/462 (10%)

Query: 2   TLVEKILSKKVGYEVCAGDSIEVEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFD 61
           TL EK+    V YE    ++  + +D  + H+ T+P A+  L+     V  P K     D
Sbjct: 4   TLYEKLFDAHVVYEA-QNETPLLYIDRHLVHEVTSPQAFDGLRAHKRPVRQPGKTFATMD 62

Query: 62  HNVPPNTVK---AAEMQKLALEFV----KRFGIK--NFHKGGEGICHQILAENYV-LPNM 111
           HNV   T     + EM ++ ++ +    K FG++  + +   +GI H +  E  V LP M
Sbjct: 63  HNVSTQTKDINASGEMARIQMQELIKNCKEFGVELYDLNHPFQGIVHVMGPEQGVTLPGM 122

Query: 112 FVAGGDSHTCTHGAFGAFATGFGATDMAYIYATGETWIKVPKTIRVDIVGKNE-NVSAKD 170
            +  GDSHT THGAFGA A G G +++ ++ AT        KT+++++ GK    ++AKD
Sbjct: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVKGKAAPGITAKD 182

Query: 171 IVLRVCKEIGRRGATYMAIEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYDY 230
           IVL +  + G  G T   +E+ GE ++++ M+GR+TLCNMAIEMG K G++  D+ T+DY
Sbjct: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDQTTFDY 242

Query: 231 LKKE----RGLSDEDIAKLKKERITVNRDEANYYKEIEIDITDMEEQVAVPHHPDNVKPI 286
           +K      +G+   D     K   T   D A +   + +   ++  QV    +P  V  +
Sbjct: 243 VKGRLHAPKGVDFADAVAYWKTLTT--DDGATFDSVVTLQAEEIAPQVTWGTNPGQVISV 300

Query: 287 SDV-------------------------------EGTEINQVFIGSCTNGRLSDLREAAK 315
           +D+                                   I++VFIGSCTN R+ DLR AA+
Sbjct: 301 TDIIPDPASFSDPVERASAEKALAYMGLKSGVPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360

Query: 316 YLKGREVHKDVKLIVIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAE 375
             KGR+V   V+ +V+P S  V  QA  EG+  IF++AG     PGC  CL  +   L  
Sbjct: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420

Query: 376 GEICLSTTNRNFKGRMGHINSYIYLASPKIAAISAVKGYITN 417
           GE C ST+NRNF+GR G      +L SP +AA +AV G+  +
Sbjct: 421 GERCASTSNRNFEGRQGR-GGRTHLVSPAMAAAAAVTGHFAD 461


Lambda     K      H
   0.318    0.136    0.399 

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: 488
Number of extensions: 22
Number of successful extensions: 4
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: 420
Length of database: 466
Length adjustment: 32
Effective length of query: 388
Effective length of database: 434
Effective search space:   168392
Effective search space used:   168392
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: 51 (24.3 bits)

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