Align β-galactosidase L+M (LacL+LacM) (EC 3.2.1.23) (characterized)
to candidate Echvi_2143 Echvi_2143 Beta-galactosidase/beta-glucuronidase
Query= CAZy::AAA25267.1 (626 letters) >FitnessBrowser__Cola:Echvi_2143 Length = 1036 Score = 337 bits (863), Expect = 2e-96 Identities = 211/633 (33%), Positives = 326/633 (51%), Gaps = 52/633 (8%) Query: 9 DDPEVFRVNQLPAHSDHHYYHDTAEFKTGSRFIKS----LNGAWRFNFAKTPAERPVDFY 64 ++P V N+LP + + Y + A + G + LNG W+F + + P DFY Sbjct: 30 ENPHVQEENRLPMRASYFPYENEALAEKGEKAASDRFFDLNGTWKFFWTDHYTKLPKDFY 89 Query: 65 QPDFDATDFDTIQVPGHIELAGYGQIQYINTLYPWEGKIYR-RPPYTLNQDQLTPGLFSD 123 FD +D QVP + E GYG Y+N +P+E + PP+ N+ Sbjct: 90 ATGFDDAAWDDFQVPANWEFNGYGTPIYVN--HPFEFAVDNPNPPFIENEK--------- 138 Query: 124 AADNTVGSYLKTFDLDDVFKGQRIIIQFQGVEEALYVWLNGHFIGYSEDSFTPSEFDLTP 183 N G Y + L D ++ Q++ I V+ A +++NG ++G EDS SEF+LT Sbjct: 139 ---NPAGVYRRKISLPDGWEDQQVFIHLGAVKSAFRLYVNGVYVGLGEDSKLESEFELTD 195 Query: 184 YIQDQGNVLAVRVYKHSTAAFIEDQDMFRFSGIFRDVNILAEPASHITDLDIRPVPNANL 243 Y+Q N++ + V + +++E QD +R SGI RDV + + P H DL ++ + Sbjct: 196 YVQPGENLITIEVRRWHDGSYLEAQDFWRISGIERDVYLYSRPKVHFYDLFVKSPLTNSY 255 Query: 244 KSGELNITTKV-------TGEPATLALTVKDHDGRVLTSQTQT--------GSGSVTFDT 288 + G+L++T + GE +A + D +G V+ QTQ G + F T Sbjct: 256 RDGKLDVTVDLWNRTDEQQGENTVMA-KLLDPNGNVVFEQTQATIGLKRKQGKTVLNFAT 314 Query: 289 MLFDQLHLWSPQTPYLYQLTIEVYDADHQLLEVVPYQFGFRTVELRDDKVIYVNNKRLVI 348 + + WS +TP LYQL + + +A + LEVV GFRT E+ ++ + VN K ++ Sbjct: 315 EI-PSVKAWSAETPTLYQLELVLANAAGEPLEVVRQNVGFRTYEVVGNQFL-VNGKAVLF 372 Query: 349 NGVNRHEWNAHTGRVISMADMRADIQTMLANNINADRTCHYPDQLPWYQLCDEAGIYLMA 408 GVNRHE + T VI+ M D++ M N+NA R HYP+ WY+LCD+ G Y++ Sbjct: 373 KGVNRHESHPETHHVITKEQMETDVRIMKELNMNAVRLSHYPNDPYWYELCDKYGFYVID 432 Query: 409 ETNLESHGSWQKMGAIEPSYNVPGDNPHWPAAVIDRARSNYEWFKNHPSIIFWSLGNESY 468 E N+ESHG + P + G+ P W A + R + KNHPS++ WS+GNE+ Sbjct: 433 EANIESHGMY-----YSPERTL-GNAPEWLHAHMLRIKRMVFRDKNHPSVVAWSMGNEAG 486 Query: 469 AGEDIAAMQAFYKEHDDSRLVHYEGVFYTPELKDRISDVESRMYEKPQNIVAYLEDNPTK 528 G + + K +D SR V YE Y + +D+ Y P +++ Y E NP + Sbjct: 487 NGYNFYKAYEWIKAYDPSRPVQYERSTY-----EWNTDIIVPQYPHPNSMIRYAESNPKR 541 Query: 529 PFLNCEYMHDMGNSLGGMQSYNDLIDKYPMYQGGFIWDFIDQALFVHDPITDQDVLRYGG 588 P++ EY H MGNS+G + Y ++I YPM QGG+IWD++DQ ++ I + V YGG Sbjct: 542 PYIMSEYAHAMGNSMGNFREYWEVIKAYPMLQGGYIWDWVDQG--IYKEIDGKRVFGYGG 599 Query: 589 DF--DERHSDYAFSGNGLMFADRTPKPAMQEVK 619 D+ + SD F NG++ ADR P EV+ Sbjct: 600 DWGPEGTPSDDNFLINGVIMADRRWNPHAYEVR 632 Lambda K H 0.320 0.138 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: 1921 Number of extensions: 115 Number of successful extensions: 7 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: 626 Length of database: 1036 Length adjustment: 41 Effective length of query: 585 Effective length of database: 995 Effective search space: 582075 Effective search space used: 582075 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: 56 (26.2 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