Align PTS system, IIABC components (characterized, see rationale)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC
Query= uniprot:Q836Y6 (722 letters) >FitnessBrowser__BFirm:BPHYT_RS02745 Length = 591 Score = 231 bits (589), Expect = 8e-65 Identities = 181/546 (33%), Positives = 260/546 (47%), Gaps = 89/546 (16%) Query: 11 QKFGKALMVVVAVMPAAGLMISIGKSLPLIDPNLGLLVTTGGVLESIGWAIIGNLHLLFA 70 Q+ G+ALM+ +AV+P AGL++ +G+ N+ ++ GG AI NL LLFA Sbjct: 10 QRLGRALMLPIAVLPVAGLLLRLGQPDVF---NIKMIADAGG-------AIFDNLPLLFA 59 Query: 71 LAIGGSWAKDRAGGAFAAGISFVLINRITGAIFGVTNEMLADEQAFTHTLFGTKIMVKGF 130 + + +AKD G A AG LI A+ N+ L Sbjct: 60 IGVAVGFAKDNNGVAGLAGAIGYLIEV---AVMKDINDKL-------------------- 96 Query: 131 FTSVLEAPALNMGVFVGIIAGFVGAMAYNKYYNYRKLPDALSFFNGKRFVPFVVILWSTI 190 NMGV GI+AG V + YN+Y + KLPD L+FF GKRFVP V + + Sbjct: 97 ----------NMGVLSGIVAGIVAGLLYNRYKDI-KLPDYLAFFGGKRFVPIVTGVVCLV 145 Query: 191 VSIALALIWPNIQAGINNFGLWIAQSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPINY 250 + IA +W +QA I+ G W+ +A L F++G L RLLL GLHH+L + Sbjct: 146 LGIAFGYVWQPVQAVIDTAGHWLT----TAGALGAFVFGVLNRLLLVTGLHHILNSLTWF 201 Query: 251 TQLGGTYEILSGAQAGTQVFGQDPLWLAWATDLVNLKGAGDMSKYQFVLENWTPARFKVG 310 + GT+ GA GD+ ++F + T F G Sbjct: 202 --VFGTFTPPGGAAV-----------------------TGDL--HRFFAGDPTAGTFMTG 234 Query: 311 QMIGSSGILMGMALAMYRNVDADKKAKYKSMYFSAALAVFLTGVTEPLEFMFMFAAVPLY 370 L LAM+ +++A + FS AL FLTGVTEP+EF FMF A LY Sbjct: 235 FFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLY 294 Query: 371 VIYAVIQGAAFAMADILPLRV---HSFGNIELLTRTPLAIKAGLGGDLINFVLMVIIFGV 427 VI+A++ G + A+ L + + S G I+ + L+ + G I V MV+ +G Sbjct: 295 VIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTR-GWWAIPIGLVYMVVYYG- 352 Query: 428 VTYFLANFLIKKFNYATPGRNGNYDNDNSEEIASGAAGS---GVVDQQIAQIVYLLGGKQ 484 L F I+KFN ATPGR ++ + A+G S G + + + LGG Sbjct: 353 ----LFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGAS 408 Query: 485 NIKEVDACMTRLRVSVKDREKVGSEEAWKRAGAMGLIVK-DNGVQAVYGPKADVLKSDIE 543 N+ VDAC TRLR+SV D KV SE K GA G++ + VQ + GP+AD++ +I Sbjct: 409 NLSVVDACTTRLRLSVVDSNKV-SENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIR 467 Query: 544 DLLASG 549 ++A G Sbjct: 468 TVIAQG 473 Score = 34.3 bits (77), Expect = 2e-05 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 7/72 (9%) Query: 460 ASGAAGSGVVDQQIAQIVYLLGGKQNIKEVDA-CMTRLRVSVK-----DREKVGS-EEAW 512 AS A GSG +D + + + GG N+ +DA TRLR+ V+ DR+++ + + AW Sbjct: 496 ASVAQGSGPLDPDPLRWLAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAW 555 Query: 513 KRAGAMGLIVKD 524 A ++V D Sbjct: 556 ISADTFHIVVGD 567 Lambda K H 0.322 0.138 0.404 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: 1075 Number of extensions: 63 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 722 Length of database: 591 Length adjustment: 38 Effective length of query: 684 Effective length of database: 553 Effective search space: 378252 Effective search space used: 378252 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 (21.9 bits) S2: 54 (25.4 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