Align aconitate hydratase; EC 4.2.1.3 (characterized)
to candidate WP_086508286.1 BZY95_RS01750 aconitate hydratase
Query= CharProtDB::CH_122731 (777 letters) >NCBI__GCF_002151265.1:WP_086508286.1 Length = 656 Score = 275 bits (704), Expect = 4e-78 Identities = 217/728 (29%), Positives = 325/728 (44%), Gaps = 98/728 (13%) Query: 59 PLTYAEKLLYGHLDDPHNQEIERGVSYLKLRPDRVACQDATAQMAILQFMSAGIPQVAT- 117 PL A++L+ HL D E+ G S + LR D+ QD + +L+ + G+ +V T Sbjct: 2 PLNLAQQLIRDHLVDG---EMTPG-SEIALRIDQALLQDVLGTLVMLELEAMGLDRVKTQ 57 Query: 118 PSTVHCDHLIQAQVGGPKDLARAIDLNKEVYDFLSTACAKYNLGFWKPGSGIIHQIVLEN 177 PS + DH L +A +LN E Y FL +AC ++ + + PG+GI H + +E+ Sbjct: 58 PSVQYIDH----------GLVQADNLNAETYLFLKSACERFGVWYSGPGNGISHPVHMEH 107 Query: 178 YAFPGALLIGTDSHTPNAGGLGQLAIGVGGADAVDVMSGLPWELKAPKIIGVKLTGKMSG 237 + PG ++G DSHT AG LG LAIG GG + M+G P L P+I G++L G + Sbjct: 108 FGIPGQSIVGCDSHTTAAGSLGMLAIGAGGIEVAMAMAGEPLYLSMPEIWGIRLAGSLPD 167 Query: 238 WTSPKDIILKLAGITTVKGGTGSIVEYFGSGVDTFSCTGMGTICNMGAEIGATTSVFPFN 297 W S KD +L+L V G +I+EY G G+ S + NMG E+GAT +VFP + Sbjct: 168 WVSAKDAVLELLRRHGVAGAKNTIIEYHGPGLANLSAMDRHVLANMGTEMGATATVFPSD 227 Query: 298 DSMVDYLNATGRSEIAQFAQVYKKDFLSADEGAEYDQVIEIDLNTLEPHINGPFTPDLAT 357 + +L A GR A + L+A+ G YD+ +DL++LEP I P +PD Sbjct: 228 EEARRFLAARGRE--ADWKP------LAAEPGCTYDREEVLDLSSLEPLIALPSSPDKVV 279 Query: 358 PVSKMKETAIANGWPLEVKVGLIGSCTNSSYEDMTRAASIIKDAGAHGLKSKALYTVSPG 417 PV ++ G PL IGS N Y D A +++ + ++P Sbjct: 280 PVREVV------GEPLH--QAYIGSSGNPGYRDFAVVAEMVR---GRTVADGVSLDINPS 328 Query: 418 SEQVRATIARDGQLKTFEDFGGVVMANACGPCIGQWDRQDIKKGDKNTIVSSFNRNFTAR 477 S QV AT+ RDG L G + C CIG + + T+ RNF R Sbjct: 329 SRQVLATLIRDGYLADLVASGARLHQTGCNGCIGMGQAPAVGRNSLRTV----PRNFPGR 384 Query: 478 NDGNPATHAFVASPEMATVYAISGDLGFNPITDTLVGADGKEFKLKEPQGVGLPPDGYDP 537 + G F+ SPE A A++G + AD + + P+ Sbjct: 385 S-GTREDSVFLCSPETAAASALAGSI-----------ADPRSLDMAYPR----------- 421 Query: 538 GENTYQAPPEDRASVEVVISPTSDRLQKLSPFKPWDG----------KDAERLPILIKAV 587 P + + +V ++P +L P + D D +P+L+ Sbjct: 422 ----IAEPAQMVVNRDVFVAPLPLAEARLKPLQKTDNTPALPELAALPDTLEVPVLLVTG 477 Query: 588 GKTTTDHISMAGPWLKYRGHLENISNNYMIGAINAENGKANEVRNHYTGKYDGVPQTAAA 647 +TD I AG + S + A++A+ + E G Sbjct: 478 DNVSTDDIMPAGQRVMPYWSSVYASAPFTFEAVDADYARRAENTRTLGGH---------- 527 Query: 648 YRDAGHKWVVIGDENFGEGSSREHAALEPRFLGGFAIITKSFARIHETNLKKQGLLPLNF 707 ++G N+G+GSSRE+AAL PR+LG A++ KSFARIH NL G LPL+F Sbjct: 528 --------AIVGGHNYGQGSSRENAALVPRYLGLQAVLAKSFARIHWQNLICFGALPLSF 579 Query: 708 KNPADYDKINFDDEVDLIGL-TTLAPGKDVILRVHPKEGEAWEAVLTHTFNSEQLEWFKH 766 + DYD++ D + + L LA G ++ V K L H Q E Sbjct: 580 IDAQDYDRLEQGDSLVIHDLHAQLAAGAELTAEVVGKGAFR----LHHGLTPRQRELLAC 635 Query: 767 GSALNFIK 774 G +N I+ Sbjct: 636 GGVINHIR 643 Lambda K H 0.316 0.134 0.401 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: 1175 Number of extensions: 65 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: 777 Length of database: 656 Length adjustment: 39 Effective length of query: 738 Effective length of database: 617 Effective search space: 455346 Effective search space used: 455346 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 (21.6 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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