Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate WP_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC
Query= SwissProt::P39816 (631 letters) >NCBI__GCF_001277175.1:WP_038857764.1 Length = 499 Score = 371 bits (953), Expect = e-107 Identities = 213/498 (42%), Positives = 306/498 (61%), Gaps = 42/498 (8%) Query: 2 FKKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVG 61 F K+ L +GRALM P+++LPAAGLLL FGDK ++P++ +AGGV+FDNLPL+FA+G Sbjct: 7 FVKSLSKLSMIGRALMLPISLLPAAGLLLAFGDK--FHLPLMMNAGGVIFDNLPLLFAIG 64 Query: 62 VAIGLAGGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPY--EGAEHL-------IDMGV 112 A+GLA G+A L+A + I+ +T+ LG+ P G ++ + MGV Sbjct: 65 SAVGLASESGIAALSAAVSVFIINITISTQ---LGITPEMAASGGKYAMVVGIPTLQMGV 121 Query: 113 FGGIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNG 172 FGG+I G+LAA+ Y RF +++L LGFFSGKRFV I + S ++G+ +VW IQ G Sbjct: 122 FGGLISGILAAWCYNRFHTLQLPEFLGFFSGKRFVAIAAAFLSFLLGLALPYVWQHIQAG 181 Query: 173 INAASSLIA--DSTVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDL 230 I+A S ++ + F + + R LIP GLHHI+Y F++ G+YT TG + GD Sbjct: 182 IDALSVIVNGDNQAASTFIFGLVERALIPLGLHHIWYPSFWYSFGDYTT-QTGQVIHGDQ 240 Query: 231 TRFFA------------GDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVM 278 T +F AG+FM G+FP M+F LPA LA+ H A + KK+ SG++ Sbjct: 241 TIWFKMLEEGVKSFSSNTYQNAGKFMQGEFPLMLFALPAACLAMYHEASTKNKKIASGIL 300 Query: 279 ISAALTSMLTGITEPVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDY 338 SAALT LTGITEPVEF+F+FVAPVLY+ N+I+AG+ ++ L +FS G IDY Sbjct: 301 FSAALTCFLTGITEPVEFTFIFVAPVLYVFNAIMAGLAYMCMYLLDAHIAKSFSAGLIDY 360 Query: 339 VLNYGL--STNGWV-----VIPVGIVFAFIYYYLFRFAILKWNLKTPGRETDEDGQNEEK 391 + ++G+ S NG+ + VGI A IYY+ FRF I ++++KTPGR D ++K Sbjct: 361 I-SFGILPSFNGYQTHYLNAVIVGIPMAIIYYFTFRFVIRRFDVKTPGR-VDVTASADDK 418 Query: 392 APVAKDQLAFHVLQALGGQQNIANLDACITRLRVTVHQPSQVCKDELKRLGAVGVLEV-N 450 +LA +++ LGG++NI ++ ACITRLR+ V +P V KD L LGA GV+ V + Sbjct: 419 TDA---ELAGNIVGLLGGKENITSVGACITRLRLEVARPDLVDKDGLNGLGARGVVFVGD 475 Query: 451 NNFQAIFGTKSDALKDDI 468 N Q IFG ++ + + Sbjct: 476 NGIQVIFGARAQFIAQSL 493 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: 832 Number of extensions: 43 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: 631 Length of database: 499 Length adjustment: 36 Effective length of query: 595 Effective length of database: 463 Effective search space: 275485 Effective search space used: 275485 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 24 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