Align β-galactosidase (GKGal1A;GK2337) (Gal1A) (EC 3.2.1.23) (characterized)
to candidate 16981 b2901 6-phospho-beta-glucosidase A (NCBI)
Query= CAZy::BAD76622.1 (455 letters) >FitnessBrowser__Keio:16981 Length = 479 Score = 435 bits (1119), Expect = e-126 Identities = 228/478 (47%), Positives = 305/478 (63%), Gaps = 29/478 (6%) Query: 5 RKSIIPDDFLWGGAVTSFQTEGAWNEGGKGLSIVDA--------------RPIPKGHSDW 50 +K +P DFLWGGAV + Q EG WN+GGKG SI D +P + Sbjct: 4 KKLTLPKDFLWGGAVAAHQVEGGWNKGGKGPSICDVLTGGAHGVPREITKEVLPGKYYPN 63 Query: 51 KVAVDFYHRYKEDIALFKELGFTAYRTSIAWTRIFPDG-EGEPNEAGLAFYDAVFDELRA 109 AVDFY YKEDI LF E+GF +RTSIAWTRIFP G E +PNE GL FYD +FDEL Sbjct: 64 HEAVDFYGHYKEDIKLFAEMGFKCFRTSIAWTRIFPKGDEAQPNEEGLKFYDDMFDELLK 123 Query: 110 NGIEPVITLYHFDLPLALAKKYNGFASRKVVDLFERYARTVFERYRGKVNYWLTFNEQNL 169 IEPVITL HF++PL L ++Y + +RKVVD F R+A VFERY+ KV YW+TFNE N Sbjct: 124 YNIEPVITLSHFEMPLHLVQQYGSWTNRKVVDFFVRFAEVVFERYKHKVKYWMTFNEINN 183 Query: 170 VLE-QPHLWGAIC-----PEDEDPEAFAYRVCHNVFIAHAKAVKALREIAPEAKIGGMVT 223 + L+G C E E+PE Y+V H+ F+A A AVKA R I PE K+G M+ Sbjct: 184 QRNWRAPLFGYCCSGVVYTEHENPEETMYQVLHHQFVASALAVKAARRINPEMKVGCMLA 243 Query: 224 YLTTYPATCRPEDAL-ANVQAKELFIDFFFDVFARGAYPRYVTNQLEKKGICLPLEAGDE 282 + YP +C P+D + A +E ++ F DV RG YP YV N+ E++G + +E GD Sbjct: 244 MVPLYPYSCNPDDVMFAQESMRERYV--FTDVQLRGYYPSYVLNEWERRGFNIKMEDGDL 301 Query: 283 ELLRSQTVDFLSFSYYQSQIVRHQEQDERIIKGLE---PNPYLPKTKWGWAIDPIGLRIA 339 ++LR T D+L FSYY + V+ + I G E PNPY+ + WGW IDP+GLR A Sbjct: 302 DVLREGTCDYLGFSYYMTNAVKAEGGTGDAISGFEGSVPNPYVKASDWGWQIDPVGLRYA 361 Query: 340 LKDVYARYEMPIFITENGIGLEEELNENGTVDDDERIDYLRRHIEQMKMAME-EGVEVIG 398 L ++Y RY+ P+FI ENG G +++ E+G+++DD RIDYLR HIE+MK A+ +GV+++G Sbjct: 362 LCELYERYQRPLFIVENGFGAYDKVEEDGSINDDYRIDYLRAHIEEMKKAVTYDGVDLMG 421 Query: 399 YLMWGATDLLS-SQGEMRKRYGVIFVNRDDENLRDLKRYKKKSFYWFQRVIRTNGEEL 455 Y WG D +S + G+ KRYG I+VN+ D+ D+ R +KKSF W++ VI +NGE+L Sbjct: 422 YTPWGCIDCVSFTTGQYSKRYGFIYVNKHDDGTGDMSRSRKKSFNWYKEVIASNGEKL 479 Lambda K H 0.321 0.140 0.430 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: 716 Number of extensions: 43 Number of successful extensions: 8 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: 455 Length of database: 479 Length adjustment: 33 Effective length of query: 422 Effective length of database: 446 Effective search space: 188212 Effective search space used: 188212 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 (21.8 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