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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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:
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