Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate CCNA_02347 CCNA_02347 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__Caulo:CCNA_02347 Length = 498 Score = 142 bits (357), Expect = 3e-38 Identities = 128/425 (30%), Positives = 194/425 (45%), Gaps = 30/425 (7%) Query: 25 VGMAVGTY----KSGKALVGRDGRTSSVMLKNAMISGLLSTGMEVLDADLIPTPALAWGT 80 +G+ +GTY K +VG D R+ S +KNA+I GL+S G EV D L +P + Sbjct: 48 LGLGLGTYIHELGQSKIVVGHDFRSYSTSIKNALILGLISAGCEVHDIGLALSPTAYFAQ 107 Query: 81 RKLADAGV-MITASHNPPTDNGVKVFNGDGTEFYVEQERGLEEIIFSGNFRKARWDEIKP 139 L V M+TASHN GVK+ F ++ L+ I+ + F + D K Sbjct: 108 FDLDIPCVAMVTASHNENGWTGVKMGAQKPLTFGPDEMSRLKAIVLNAEFVER--DGGKL 165 Query: 140 VRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLVAPYLLREMG-AKVLSVNAHVDG 198 +R YI+ V LKV+ NG L++MG A+V+ ++ +D Sbjct: 166 IRVQGEAQRYIDDVAKRASVTRPLKVIAACGNGTAGAFVVEALQKMGVAEVVPMDTDLDF 225 Query: 199 HFPGRKPEPR-YENIAYLGKLVRELGVDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFA 257 FP P P E + + VRE G DLA DGD DR V D++G + D + + A Sbjct: 226 TFPKYNPNPEDAEMLHAMADAVRETGADLAFGFDGDGDRCGVVDDEGEEIFADKIGLMLA 285 Query: 258 KLYVEEHGGGTVVVSIDTGS--RIDAVVERAGGRVVRIPLGQPHDGIKRYKAIFAA---- 311 + H G T VV + + D ++ + G +V+ G H IKR A A Sbjct: 286 RDLAPLHPGATFVVDVKSTGLYATDPILAQHGCKVIYWKTG--HSYIKRKSAELGALAGF 343 Query: 312 --EPWKLVHPKFGPWIDPFVTMGLLIKLIDENGP---LSELVKEIPTYYLKKA-NVLCPD 365 ++ + G D +T I + + P LS++ K +P + + C D Sbjct: 344 EKSGHFFMNGELGYGYDCGLTAAAAILAMLDRNPGVKLSDMRKALPVAFTSLTMSPHCGD 403 Query: 366 EYKAEVVRRAAEEVERK-------LSSEIKEVLTISGFRIALNDGSWILIRPSGTEPKIR 418 E K VV +E E L +I EV+T++G R+ L DGSW+L+R S +P++ Sbjct: 404 EVKYGVVADVVKEYEDLFAAGGSILGRKITEVITVNGVRVHLEDGSWVLVRASSNKPEVV 463 Query: 419 VVAEA 423 VV E+ Sbjct: 464 VVVES 468 Lambda K H 0.318 0.138 0.402 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: 563 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 450 Length of database: 498 Length adjustment: 33 Effective length of query: 417 Effective length of database: 465 Effective search space: 193905 Effective search space used: 193905 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: 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