Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AZOBR_RS18900 AZOBR_RS18900 peptidase
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__azobra:AZOBR_RS18900 Length = 766 Score = 251 bits (641), Expect = 1e-70 Identities = 192/612 (31%), Positives = 299/612 (48%), Gaps = 32/612 (5%) Query: 234 EDAEAAIKALVALLAEGCGEAVVNVAEPVATQSSATL---LRGVCASPGSAFGQVVQVTD 290 E + + L+A+G +VN E +T A L L G + G A G V + Sbjct: 159 ETLQTIAMVVAELVAQG---ELVNPQEVASTGDPALLPARLSGTSLASGLAMGLAV-IHR 214 Query: 291 PELVITEQGTGGA-TERAALTRGLLAANEALQVLQDKAAGSAQAE---IFRAHQELLEDP 346 P+L I + + A +E A L + + A+ L + AA + +E I ++ ED Sbjct: 215 PQLTIRQMVSEDAESELARLNAAIATMHSAIDDLLNAAALAGLSEPKDILETYRMFAEDR 274 Query: 347 TLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGI 406 L + G +A A T L + I ER DL D+ R+L+ + G Sbjct: 275 GWLSRIREAIRMGLTAEGAVQQVQNDTRARMSHLTDPYIRERLLDLEDLTNRLLQHLAGR 334 Query: 407 QDSA--WDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAIC 464 + A LPE +L+A + P++ D R++ G + G +SHV I+ARAL +P + Sbjct: 335 KSEADGGTLPEDIVLVARSMGPAELLDYDQRRLRGVILEEGSPSSHVCIVARALNIPVV- 393 Query: 465 GVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQA--SLPA 522 P + + V++D D G+ + P AE Q+ A + + + +A + P+ Sbjct: 394 QAPDALNRIEPLDPVIVDGDHGQAFVRP--AEDIQMAFAEAVALRARKEQMYEAIRAQPS 451 Query: 523 TTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIA 582 TRDG + + N L ++ H G EG+GL R+E ++ R+ P Q Y+ I Sbjct: 452 VTRDGVPISIQLNCGLLIDLPHLKASGAEGIGLYRTEIPFMVRSTYPDVHAQTDLYSRIL 511 Query: 583 RALGTERNLVVRTLDVGGDKPLAYVPM-DAETNPFLGLRGIRLCLERPQLLREQFRAILA 641 ++ +V RTLDVGGDK L Y+ + E NP LG R IR+ L+ P LLR+Q RA+L Sbjct: 512 DQTD-DKPVVFRTLDVGGDKMLPYIAASEGEENPALGWRAIRIGLDHPSLLRQQLRALLR 570 Query: 642 SAGFARLHIMLPMVSLLSELHLARKILEEEALAL-GLTELP----KLGIMIEVPSAALMA 696 ++ L +M PM++ ++E AR++L+ E L G P ++G MIEVP+ Sbjct: 571 ASAGRPLSVMFPMIAEVAEFDAARRLLDLEINRLKGQGGEPPSRVRVGTMIEVPALLWQL 630 Query: 697 DVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWV 756 P VDF S+G+NDLTQY A DR +PR + + D PA++ L+ V+A G V Sbjct: 631 PALLPRVDFLSVGSNDLTQYIFASDRGNPRTSGRYDPLSPAMMSLLRRLVEACGDAGVPV 690 Query: 757 GVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLG---LE 813 +CG +A L LIG+G LS+S P + +K +R LD+A + RQ + L Sbjct: 691 SICGEMAGRPLDAMALIGIGFRTLSMSPPSVGPVKTMLRSLDVA----VLRQYMNGLYLR 746 Query: 814 EAAEVREALRQY 825 +R+ LR + Sbjct: 747 GDHSLRDKLRSF 758 Lambda K H 0.318 0.133 0.371 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: 1343 Number of extensions: 64 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: 838 Length of database: 766 Length adjustment: 41 Effective length of query: 797 Effective length of database: 725 Effective search space: 577825 Effective search space used: 577825 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: 55 (25.8 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