GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Herbaspirillum seropedicae SmR1

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate HSERO_RS16515 HSERO_RS16515 isopropylmalate isomerase

Query= curated2:Q8TLF1
         (424 letters)



>FitnessBrowser__HerbieS:HSERO_RS16515
          Length = 466

 Score =  231 bits (588), Expect = 5e-65
 Identities = 156/441 (35%), Positives = 220/441 (49%), Gaps = 55/441 (12%)

Query: 38  VDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPFDHIAPANNETS------ATLQREI 91
           +D  + H+ TS  A    K +   + W  S  ++  DH  P  +         + LQ E 
Sbjct: 27  IDRHLLHEVTSPQAFEGLK-LAGRQPWRNSANLMVADHNVPTTDRAHGIADPISRLQVET 85

Query: 92  REW-VKEQGIPNF--YEVGEGICHQVLPENGFALPGKLVVGADSHSCTYGAFGAFATGVG 148
            +   KE  +  F   +  +GI H + PE G  LPG  VV  DSH+ T+GAF A A G+G
Sbjct: 86  LDGNAKEYSLTYFGMNDKRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFAALAHGIG 145

Query: 149 ATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYAKDLTLYLIGKTGIAGATYKAVEFYG 208
            +++  + AT  L  +  ++  + V+G+L  GV AKD+ L +IGK G AG T  A+EF G
Sbjct: 146 TSEVEHVLATQTLLARKSKAMLVQVDGALPAGVTAKDIVLAVIGKIGTAGGTGYAIEFAG 205

Query: 209 QAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTFEFLK-----------NRAAATYEPV 257
             IR L++ GRMT+CNMAIE GA+ G+V  D+ T E+LK            RA + +  +
Sbjct: 206 STIRSLSMEGRMTVCNMAIEAGARAGMVAFDDTTLEYLKGRPFSPSGPHWERAVSYWRSL 265

Query: 258 YADPDAVYLEEFTYDADDIEPQV---ACPHQVDNV------------------------- 289
           ++DP A +    T +A +I+PQV     P  V  V                         
Sbjct: 266 HSDPGAKFDMVVTLNAAEIKPQVTWGTSPEMVVAVDARVPDPDKEKDPTKRDGMEKALAY 325

Query: 290 ---KPVGEVEGTHVDQVFIGTCTNGRLEDLEVAAAVLKGKQVAVR---TIVIPASRTTLL 343
              KP   +E   +D+VFIG+CTN R+EDL  AA V++GK  A      +V+P S     
Sbjct: 326 MALKPNTPIEDIRIDKVFIGSCTNSRIEDLREAAKVVRGKFRASNVKLAMVVPGSGLVKE 385

Query: 344 AAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKGGFIYL 403
            A   G  +    AG     PGC  CL  +   L  GE C ST+NRNF+GR G GG  +L
Sbjct: 386 QAEREGLDKIFRDAGFEWREPGCSMCLAMNADRLEPGERCASTSNRNFEGRQGAGGRTHL 445

Query: 404 ASPATAAASALTGEITDPRTV 424
            SPA AAA+ + G   D R++
Sbjct: 446 VSPAMAAAAGIAGHFVDVRSL 466


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: 451
Number of extensions: 14
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: 466
Length adjustment: 32
Effective length of query: 392
Effective length of database: 434
Effective search space:   170128
Effective search space used:   170128
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