Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate Pf1N1B4_4621 L-arabonate dehydratase (EC 4.2.1.25)
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4621 Length = 578 Score = 441 bits (1135), Expect = e-128 Identities = 260/599 (43%), Positives = 356/599 (59%), Gaps = 26/599 (4%) Query: 1 MSDTPKHRLRSEQWFNDPAHADMTALYVERYM-NYGMTREELQSGRPIIGIAQTGSDLTP 59 MSD K LRS QWF AD +M N G+ + G+PIIGI T S+LTP Sbjct: 1 MSDK-KPTLRSAQWFGT---ADKNGFMYRSWMKNQGIADHQFH-GKPIIGICNTWSELTP 55 Query: 60 CNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPL 119 CN H ++A+ VK G+ +AGG P+EFPV E + RPTA L RNLA + + E + G P+ Sbjct: 56 CNAHFRQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPI 115 Query: 120 DGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAA 179 DGVVL TGCDKTTPA LM AA+ D+PAIV++GGPML+G HKG+ IGSGTV+W + A Sbjct: 116 DGVVLLTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKA 175 Query: 180 GEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAY 239 G I + F+ S S G CNTMGTA +M +AEALG SLP A+IPA R +A+ Sbjct: 176 GTITLDDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAH 235 Query: 240 ATGKRICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLED 299 +G R ++VR+D++ S+I+T++AFENAI V +A+G S+N HL AIA +GVEL L+D Sbjct: 236 MSGMRAVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDD 295 Query: 300 WQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRL-HEDCATVSGKTIGEI 358 W RIG +P +V+ P+G++L E F+ AGG+P+V+ L +A + + + TV+GKTIGE Sbjct: 296 WSRIGRGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKTIGEN 355 Query: 359 VSNS-LTSNTDVIHPFDTPLKHRAGFIVLSGNFFD-SAIMKMSVVGEAFRKTYLSEPGAE 416 ++ + +VI D P++ G VL GN A++K S + Sbjct: 356 TKDAPIYGQDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAASAELMQ--------- 406 Query: 417 NSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIK 476 RA+VFE + Y ARI+DP LD+D ILV++ G GYPG AEV NM PA L+ Sbjct: 407 --HRGRAVVFENFDMYKARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLA 464 Query: 477 QGIDSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDD 536 QG+ + + D R SGT+ +L+++PEAA GG LA +K D +++D ++L I D Sbjct: 465 QGVTDMVRISDARMSGTAYGTVVLHVAPEAAAGGPLATVKEGDWIELDCANGRLHLDIPD 524 Query: 537 AEMAQRRREWIPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGE-PRHSH 594 AE+A R + P +++LY V Q G V R E PRHSH Sbjct: 525 AELAARMADLQPPQQLIVGGYRQLYIDHVLQADQG-----CDFDFLVGCRGAEVPRHSH 578 Lambda K H 0.319 0.135 0.407 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: 964 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: 594 Length of database: 578 Length adjustment: 37 Effective length of query: 557 Effective length of database: 541 Effective search space: 301337 Effective search space used: 301337 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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