Align sucrose phosphorylase (GtfA;SMU.881) (EC 2.4.1.7) (characterized)
to candidate 15429 b1309 putative polysaccharide hydrolase (VIMSS)
Query= CAZy::AAN58596.1 (481 letters) >FitnessBrowser__Keio:15429 Length = 559 Score = 207 bits (527), Expect = 7e-58 Identities = 152/480 (31%), Positives = 228/480 (47%), Gaps = 49/480 (10%) Query: 8 MLITYADSLGKN----LKELNENIENYFGDAVGGVHLLPFFPSTGDRGFAPIDYHEVDSA 63 +LITYAD N L N+ + VHLLPF+P + D GF+ IDYH+V S Sbjct: 50 VLITYADQFHSNDLKPLPTFNQFYHQWLQSIFSHVHLLPFYPWSSDDGFSVIDYHQVASE 109 Query: 64 FGDWDDVKCLGEKYYLMFDFMINHISRQSKYYKDYQEKHEASAYKDLFLNWDKFWPKNRP 123 G+W D++ LGE +LMFDF+ NH+S +S+++K+Y ++H ++D F+ D Sbjct: 110 AGEWQDIQQLGECSHLMFDFVCNHMSAKSEWFKNYLQQH--PGFEDFFIAVD-------- 159 Query: 124 TQEDVDLIYKRKDRAPKQEIQFADGSVEHLWNTFGEEQIDLDVTKEVTMDFIRSTIENLA 183 Q D+ + + + Q D S HLW TF ++QIDL+ + + + Sbjct: 160 PQTDLSAVTRPRALPLLTPFQMRDHSTRHLWTTFSDDQIDLNYRSPEVLLAMVDVLLCYL 219 Query: 184 ANGCDLIRLDAFAYAVKKLDTNDFFVEPE--IWTLLDKVRDIAAVSGAEILPEI---HEH 238 A G + +RLDA + K+ T+ +E I LL + D A G I+ E H+ Sbjct: 220 AKGAEYVRLDAVGFMWKEPGTSCIHLEKTHLIIKLLRSIIDNVA-PGTVIITETNVPHKD 278 Query: 239 YTIQFKIADHD-YYVYDFALPMVTLYSLYSSKVDRLAKW-----LKMSPMKQFTTLDTHD 292 F D + + VY F+LP + L+++ V+ L W L S F L +HD Sbjct: 279 NIAYFGAGDDEAHMVYQFSLPPLVLHAVQKQNVEALCAWAQNLTLPSSNTTWFNFLASHD 338 Query: 293 GIGVVDVKDILTDEEITYTSNELYKVGANVNRKYSTAEYNNLD----IYQINSTYYSAL- 347 GIG+ ++ +L + EI L + GA VN K NN D Y+IN TY AL Sbjct: 339 GIGLNPLRGLLPESEILELVEALQQEGALVNWK------NNPDGTRSPYEINVTYMDALS 392 Query: 348 ----GDDDQ--KYFLARLIQAFAPGIPQVYYVGFLAGKNDLELLESTKEGRNINRHYYSS 401 D+++ ++ LA I PG+P +Y L +ND +E R INR Y S Sbjct: 393 RRESSDEERCARFILAHAILLSFPGVPAIYIQSILGSRNDYAGVEKLGYNRAINRKKYHS 452 Query: 402 EEIAKE------VKRPVVKALLNLFTYRNQSAAFDLDGRIEVETPNEATIVIERQNKDGS 455 +EI +E ++ V L L T R F D ++T N + + I R N DG+ Sbjct: 453 KEITRELNDEATLRHAVYHELSRLITLRRSHNEFHPDNNFTIDTINSSVMRIPRSNADGN 512 Lambda K H 0.318 0.136 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: 598 Number of extensions: 32 Number of successful extensions: 6 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: 481 Length of database: 559 Length adjustment: 35 Effective length of query: 446 Effective length of database: 524 Effective search space: 233704 Effective search space used: 233704 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: 52 (24.6 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