GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Marinobacter adhaerens HP15

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate GFF1877 HP15_1834 protein containing 3-isopropylmalate dehydratase, large subunit region domain

Query= curated2:Q8TLF1
         (424 letters)



>FitnessBrowser__Marino:GFF1877
          Length = 472

 Score =  236 bits (601), Expect = 1e-66
 Identities = 152/442 (34%), Positives = 225/442 (50%), Gaps = 58/442 (13%)

Query: 38  VDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPFDHIAPANNE----------TSATL 87
           +D  + H+ TS  A    + +   K W     +   DH  P  +            S   
Sbjct: 28  IDRQLLHEVTSPQAFEGLR-LAGRKPWRIDANIATPDHNVPTTDRDRGVEGIVDPVSRIQ 86

Query: 88  QREIREWVKEQGIPNFY--EVGEGICHQVLPENGFALPGKLVVGADSHSCTYGAFGAFAT 145
              + +   E GI  F   +  +GI H + PE G  LPG  +V  DSH+ T+GAFG  A 
Sbjct: 87  VETLDKNCDEFGILEFKIKDQRQGIVHVIGPEQGATLPGMSIVCGDSHTSTHGAFGCLAH 146

Query: 146 GVGATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYAKDLTLYLIGKTGIAGATYKAVE 205
           G+G +++  + AT  L  +  ++  + V G L  GV  KD+ L +IGK G AG T  A+E
Sbjct: 147 GIGTSEVEHVLATQCLVQQKMKNMLVKVNGKLGPGVTGKDVVLAIIGKIGTAGGTGHAIE 206

Query: 206 FYGQAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTFEFLKNR-----------AAATY 254
           F G+AIR L++ GRMT+CNM+IE GA+ G+V  D+ T E+++NR           A   +
Sbjct: 207 FGGEAIRGLSMEGRMTICNMSIEAGARVGMVAVDDTTIEYVRNRPFGPKGEQWDAAVEYW 266

Query: 255 EPVYADPDAVYLEEFTYDADDIEPQVAC-----------------PHQVDNVKPVGEVEG 297
             +++D DAV+ +    +  +I+PQV+                    + D +K  G V  
Sbjct: 267 RTLHSDSDAVFDKIVELEGSEIQPQVSWGTSPEMVAGIDGKVPDPEQEADPIKREGIVRA 326

Query: 298 --------------THVDQVFIGTCTNGRLEDLEVAAAVLKGKQVA---VRTIVIPASRT 340
                           +D+VFIG+CTN R+EDL  AAAV+KG++V+    + +V+P S  
Sbjct: 327 LKYMGLQPNMAITDIKLDRVFIGSCTNSRIEDLREAAAVVKGRKVSPILKQAMVVPGSGL 386

Query: 341 TLLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKGGF 400
               A + G  +  ++AG+    PGC  CL  +   LG+GE C ST+NRNF+GR G GG 
Sbjct: 387 VKAQAEQEGLDKIFIEAGLEWRDPGCSMCLAMNADKLGQGEHCASTSNRNFEGRQGFGGR 446

Query: 401 IYLASPATAAASALTGEITDPR 422
            +L SPA AAA+A+TG   D R
Sbjct: 447 THLVSPAMAAAAAVTGHFVDVR 468


Lambda     K      H
   0.318    0.135    0.400 

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: 503
Number of extensions: 26
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: 424
Length of database: 472
Length adjustment: 33
Effective length of query: 391
Effective length of database: 439
Effective search space:   171649
Effective search space used:   171649
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.

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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