Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__BFirm:BPHYT_RS02745 Length = 591 Score = 434 bits (1117), Expect = e-126 Identities = 237/503 (47%), Positives = 318/503 (63%), Gaps = 31/503 (6%) Query: 6 FQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVGVAIG 65 F +Q+LGRALM P+AVLP AGLLLR G D+ NI +I DAGG +FDNLPL+FA+GVA+G Sbjct: 6 FLKIQRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVG 65 Query: 66 LA-GGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGLLAAY 124 A GVAGLA IGYLI + ++ L +MGV GI+ G++A Sbjct: 66 FAKDNNGVAGLAGAIGYLIEVAVMKDINDKL-------------NMGVLSGIVAGIVAGL 112 Query: 125 LYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASS-LIADS 183 LY R+ I+L L FF GKRFVPI+T V LV+G+ F +VW +Q I+ A L Sbjct: 113 LYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAG 172 Query: 184 TVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDPTAGRF 243 +G F + + RLL+ GLHHI + +F+ G +T P G VTGDL RFFAGDPTAG F Sbjct: 173 ALGAFVFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPG-GAAVTGDLHRFFAGDPTAGTF 231 Query: 244 MMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSFLFVAP 303 M G FP M+F LPA LA+ H A E++ ++ G++ S ALTS LTG+TEP+EFSF+F+AP Sbjct: 232 MTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAP 291 Query: 304 VLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTNGWVVIPVGIVFAFIYY 363 VLY+I+++L G+ +C + G+TFS G IDYVLNYGLST GW IP+G+V+ +YY Sbjct: 292 VLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPIGLVYMVVYY 351 Query: 364 YLFRFAILKWNLKTPGRE-------TDEDGQNEEKAPVAKDQL--AFHVLQALGGQQNIA 414 LFRF I K+N+ TPGRE D +PVA + A + ALGG N++ Sbjct: 352 GLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLS 411 Query: 415 NLDACITRLRVTVHQPSQVCKDELKRLGAVGVLE-VNNNFQAIFGTKSDALKDDIKTIMA 473 +DAC TRLR++V ++V ++ELK +GA GVL+ + N Q I G ++D + D+I+T++A Sbjct: 412 VVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVIA 471 Query: 474 GG-----VPATAAALDTVTDKPL 491 G PA AA V P+ Sbjct: 472 QGGGDAVKPAAAAPAQVVAAAPV 494 Score = 32.0 bits (71), Expect = 8e-05 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 7/86 (8%) Query: 393 PVAKDQLAFHVLQALGGQQNIANLDA-CITRLRVTVHQPSQVCKDELKRLGAVGVLEVNN 451 P+ D L + L GG N+ +LDA TRLR+ V PS V + L L + + Sbjct: 504 PLDPDPLRW--LAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAWISA--D 559 Query: 452 NFQAIFGTKSDALKDDI--KTIMAGG 475 F + G + + + +T +GG Sbjct: 560 TFHIVVGDAAQRYAEKLATRTTQSGG 585 Lambda K H 0.324 0.142 0.421 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: 1000 Number of extensions: 49 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 631 Length of database: 591 Length adjustment: 37 Effective length of query: 594 Effective length of database: 554 Effective search space: 329076 Effective search space used: 329076 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 53 (25.0 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