Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate Pf1N1B4_2122 Phosphomannomutase (EC 5.4.2.8) / Phosphoglucomutase (EC 5.4.2.2)
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2122 Length = 465 Score = 719 bits (1856), Expect = 0.0 Identities = 355/459 (77%), Positives = 404/459 (88%), Gaps = 2/459 (0%) Query: 6 APTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELV 65 AP P SIFRAYDIRG V + L AETAYW+GRAIGS+SLA+ EP V+VGRDGRLSGPELV Sbjct: 8 APKFPDSIFRAYDIRGTVPEFLNAETAYWLGRAIGSQSLAQNEPNVSVGRDGRLSGPELV 67 Query: 66 KQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGET 125 +QLI+GL D GC VSDVG+VPTP LYYAANVL GKSGVMLTGSHNP +YNGFKIV+AG+T Sbjct: 68 EQLIKGLADSGCHVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSNYNGFKIVIAGDT 127 Query: 126 LANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAG 185 LANEQIQAL +R++ N+L+SG GS+ QV+IL RY +I DI +A+ +KVVVDCGNG AG Sbjct: 128 LANEQIQALHDRLKTNNLSSGKGSITQVEILDRYNTEIVQDIKLARRLKVVVDCGNGAAG 187 Query: 186 VIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDG 245 VIAPQLIEAL C VIPL+CEVDGNFPNHHPDPGKPENL DLIAKVK NADLGLAFDGDG Sbjct: 188 VIAPQLIEALNCEVIPLFCEVDGNFPNHHPDPGKPENLVDLIAKVKETNADLGLAFDGDG 247 Query: 246 DRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWK 305 DRVGVVTNTG+I++PDRLLMLFA+DVV+RNP A+IIFDVKCTRRLI LI YGGRP+MWK Sbjct: 248 DRVGVVTNTGSIVFPDRLLMLFARDVVARNPDAEIIFDVKCTRRLIPLIKEYGGRPLMWK 307 Query: 306 TGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFS 365 TGHSLIKKKMK++GALLAGEMSGH+FFKERWFGFDDGIY+AARLLEILS+++ +E +F+ Sbjct: 308 TGHSLIKKKMKQSGALLAGEMSGHIFFKERWFGFDDGIYAAARLLEILSKEKSTAEELFA 367 Query: 366 AFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEG-NITTLDGVRVDYPKGWGLVRASN 424 FP+DISTPEINI VTE+SKF+II+AL DAQWGEG ++TT+DGVRVDY KGWGLVRASN Sbjct: 368 TFPNDISTPEINIHVTEESKFSIIDAL-HDAQWGEGADLTTIDGVRVDYAKGWGLVRASN 426 Query: 425 TTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 TTPVLVLRFEAD E EL+RIK VF QLK V L +PF Sbjct: 427 TTPVLVLRFEADDEAELQRIKDVFHVQLKRVAPDLQLPF 465 Lambda K H 0.319 0.138 0.410 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: 703 Number of extensions: 19 Number of successful extensions: 2 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: 463 Length of database: 465 Length adjustment: 33 Effective length of query: 430 Effective length of database: 432 Effective search space: 185760 Effective search space used: 185760 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: 51 (24.3 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