GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Acidovorax sp. GW101-3H11

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate Ac3H11_1525 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)

Query= curated2:Q8TLF1
         (424 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1525
          Length = 473

 Score =  237 bits (605), Expect = 5e-67
 Identities = 157/448 (35%), Positives = 220/448 (49%), Gaps = 67/448 (14%)

Query: 38  VDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPFDHIAPAN-------------NETS 84
           +D  + H+ TS  A    +E    KVW  S IV   DH  P               ++  
Sbjct: 27  IDRHLVHEVTSPQAFEGLREAG-RKVWRMSSIVGTADHNTPTTGWEHGYDGITDPISKEQ 85

Query: 85  ATLQREIREWVKEQGIPNFYEVGEGICHQVLPENGFALPGKLVVGADSHSCTYGAFGAFA 144
            T   +    +       F    +GI H + PENG  LPG  VV  DSH+ T+GAFGA A
Sbjct: 86  ITTLNDNMATISPAAFFPFMHKRQGIVHVIGPENGATLPGMTVVCGDSHTSTHGAFGALA 145

Query: 145 TGVGATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYAKDLTLYLIGKTGIAGATYKAV 204
            G+G +++  + AT  L  K  ++  + V+G+L KGV  KD+ L +IGK G AG T   +
Sbjct: 146 HGIGTSEVEHVMATQTLLAKKAKNMLVQVDGTLAKGVTPKDVVLAIIGKIGTAGGTGYTI 205

Query: 205 EFYGQAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTFEFLKNR-----------AAAT 253
           EF G   R +++ GRMT+CNMAIE GA+ G+V  D+KT E++K R           A A 
Sbjct: 206 EFAGSVFRAMSMEGRMTVCNMAIEGGARAGLVAVDDKTIEYVKGRPLSPTGVEWDQAVAY 265

Query: 254 YEPVYADPDAVYLEEFTYDADDIEPQV---ACPHQVDNV--------------------- 289
           ++ +++D DA +      DA +I+PQV     P  V  +                     
Sbjct: 266 WKTLHSDADAQFDTVVKLDAAEIQPQVTWGTSPEMVLGIDARVPDPDKEKDANKRGAIER 325

Query: 290 ----------KPVGEVEGTHVDQVFIGTCTNGRLEDLEVAAAVLK--GKQVAVR---TIV 334
                     KP+ ++    +D+VFIG+CTN R+ED+  AAAV+K  G++VA      +V
Sbjct: 326 ALTYMDLQPGKPINDIT---IDKVFIGSCTNSRIEDMREAAAVVKNLGRKVASNVKLALV 382

Query: 335 IPASRTTLLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGR 394
           +P S      A   G  +    AG     PGC  CL  +   L  GE C ST+NRNF+GR
Sbjct: 383 VPGSGLVKEQAEREGLDQIFKAAGFEWREPGCSMCLAMNADRLEPGERCASTSNRNFEGR 442

Query: 395 MGKGGFIYLASPATAAASALTGEITDPR 422
            G GG  +L SPA AAA+A+ G   D R
Sbjct: 443 QGAGGRTHLVSPAMAAAAAVHGHFVDIR 470


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: 491
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 424
Length of database: 473
Length adjustment: 33
Effective length of query: 391
Effective length of database: 440
Effective search space:   172040
Effective search space used:   172040
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