Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_048065635.1 MA_RS16705 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000007345.1:WP_048065635.1 Length = 432 Score = 429 bits (1102), Expect = e-124 Identities = 212/420 (50%), Positives = 298/420 (70%), Gaps = 6/420 (1%) Query: 1 MVKEDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIK 60 ++ ++ +PK WYN++ DLP P+ PP DP+ D L I PK ++ Q+ + +RYI Sbjct: 6 IILDENEMPKKWYNVLADLPSPIDPPLDPRTWQPISPDALEPIFPKALIMQEMSSDRYID 65 Query: 61 IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120 IPEEV D Y + RP+PLFRA +LE+ LK+PA+IY+KYEG +P GSHK NT+I QAY+ Sbjct: 66 IPEEVLDVY-RLWRPSPLFRAHQLEKVLKSPAKIYYKYEGVSPAGSHKTNTSIAQAYYNM 124 Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180 +EG E + TETGAGQWG+A++LA + ++++ ++MV+ S+ QKP R+S++ L+G NV S Sbjct: 125 KEGTERLTTETGAGQWGSALSLACNYFDLECKVYMVRSSFYQKPYRKSLITLWGGNVVPS 184 Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKNE-FRYLVGSVLDVVLLHQSVIGQE 239 P+ TE+GRKIL+ P PGSLGIA+SEA+E A+ +E +Y +GSVL+ V+LHQ+VIG E Sbjct: 185 PSPDTEFGRKILQEQPDTPGSLGIAISEAVEDAIAHENTKYSLGSVLNHVVLHQTVIGAE 244 Query: 240 TITQLDLLGEDADILIGCVGGGSNFGGFTYPFIGN----KKGKRYIAVSSAEIPKFSKGE 295 QL + E D++IGC GGGSN GG FI + K R +AV + P +KGE Sbjct: 245 CKQQLAQVEEYPDVVIGCCGGGSNLGGIGLEFIKDRLEGKHSARVVAVEPSACPSLTKGE 304 Query: 296 YKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNER 355 Y+YDF D+A + PL+KM TLG +VPP I+AGGLRYHG +P +S L EG++E Y+++ Sbjct: 305 YRYDFGDTAEMTPLLKMYTLGHKHVPPAIHAGGLRYHGDSPIISKLCSEGLMEAVSYDQQ 364 Query: 356 EIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYE 415 E+F+AA F +GIVPAPES+HAIR +DEA+ A++ E K I+FNLSGHG D+S+Y+ Sbjct: 365 EVFDAAVQFARTEGIVPAPESSHAIRCAIDEALAAKQTGEEKTILFNLSGHGHFDMSSYD 424 Lambda K H 0.318 0.138 0.403 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: 492 Number of extensions: 18 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: 425 Length of database: 432 Length adjustment: 32 Effective length of query: 393 Effective length of database: 400 Effective search space: 157200 Effective search space used: 157200 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: 51 (24.3 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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