GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Burkholderia phytofirmans PsJN

Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate BPHYT_RS13520 BPHYT_RS13520 isopropylmalate isomerase

Query= SwissProt::Q9ZNE0
         (418 letters)



>FitnessBrowser__BFirm:BPHYT_RS13520
          Length = 471

 Score =  210 bits (534), Expect = 8e-59
 Identities = 156/475 (32%), Positives = 227/475 (47%), Gaps = 71/475 (14%)

Query: 3   QTLAEKIL-SHKVGRPVRAGELVVVEVDQVMVVDSIAGSFFKRLEYLEATPRYPERVSIV 61
           +TL +K++ SH V R       V++ VD  ++ +  +   F  L       R P++   V
Sbjct: 4   RTLYQKLVDSHVVTRVDEQN--VLLYVDLHLMNEYTSPQAFSALAAKTRRVRRPKQQLAV 61

Query: 62  IDHVAPAANLEVAKAQKEIREWGK------------RHGIRVF---DVGRGVCHQVLIEE 106
           + H+ P      A+A + IR+                 GI +    D  +G+ H V  E 
Sbjct: 62  VSHIIPTH----AEAPRVIRDAASLLLANNLARNCAEAGIALHAANDPLQGIEHIVAPER 117

Query: 107 GLAQPGWVVVGSDSHSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRGRLP 166
           GL +PG VV+  DSH+TTYGA+GA G G+G +++    A+     RV +++++   G +P
Sbjct: 118 GLVRPGMVVLCGDSHTTTYGALGALGFGIGTSEVEHVLATQTLVYRVAQTMRITIEGPMP 177

Query: 167 KGVTAKDAALEMVRLLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAGLVV 226
            G ++KD  L ++  + A+GA   AVE      A +L+   RMTL N+TVEAGA+A L+ 
Sbjct: 178 YGTSSKDLILWIISRIGAQGARGYAVEFAGSTIA-SLSAEARMTLCNMTVEAGARAALIA 236

Query: 227 PSGEILEMYR--------------VPDW--LYPDPDARYAKEVEIDLSALTPRVSVPFYV 270
           P     +  R              + DW  L  DP AR+  E   D   ++P V+     
Sbjct: 237 PDATTFDYIRAHATQLDEIAWYAAMSDWRELKSDPGARFDSEYRFDACDISPFVTWGTSP 296

Query: 271 DNVHEVAQ-------------------------------VKGKRVDQVFIGTCTNGRIED 299
           D    V +                               + G  +D+VFIG+CTNGRIED
Sbjct: 297 DQAIAVDERIPAAAAQKTPEAAAALRRALDYIGLDADQPIAGTPIDRVFIGSCTNGRIED 356

Query: 300 LRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPGCGPCMGRH 359
           LR  A ++ GR VA  VR +VVP S  V  +A  +G   TL EAG     PGC  C+  +
Sbjct: 357 LRIVASIVAGRHVAQGVRAMVVPGSGSVRRQAEAEGVAATLREAGFEWREPGCSMCLAMN 416

Query: 360 MGVLAPGEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYLTTPEELEEE 414
              L PGE C ST+NRNF GR G      +L SP +AAA+A+ G +T    LE +
Sbjct: 417 DDFLTPGERCASTTNRNFEGRQGR-GGRTHLMSPAMAAAAALTGRITDVRTLETQ 470


Lambda     K      H
   0.318    0.135    0.393 

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: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 418
Length of database: 471
Length adjustment: 32
Effective length of query: 386
Effective length of database: 439
Effective search space:   169454
Effective search space used:   169454
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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