Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate 15223 b1101 fused glucose-specific PTS enzymes: IIB component/IIC component (NCBI)
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__Keio:15223 Length = 477 Score = 418 bits (1075), Expect = e-121 Identities = 229/476 (48%), Positives = 318/476 (66%), Gaps = 14/476 (2%) Query: 1 MFKKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIP-----IIKDAGGVVFDNLP 55 MFK AF LQ++G++LM PV+VLP AG+LL G + +P ++ +AGG VF N+P Sbjct: 1 MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMP 60 Query: 56 LIFAVGVAIGLAGGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYE-GAEHLIDMGVFG 114 LIFA+GVA+G +GV+ LAAV+ Y I+ T+ + L+ P E ++HL D GV G Sbjct: 61 LIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLG 120 Query: 115 GIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGIN 174 GII G +AAY++ RF I+L LGFF+GKRFVPII+ ++++ GV+ SF+WP I + I Sbjct: 121 GIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQ 180 Query: 175 AASSLIA--DSTVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTR 232 S A + V Y I R L+PFGLHHI+ PF +GEYT+ + G GD+ R Sbjct: 181 TFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTN-AAGQVFHGDIPR 239 Query: 233 FFAGDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITE 292 + AGDPTAG+ + G F + ++ LPA A+AI H+A+PE + + G+MISAALTS LTGITE Sbjct: 240 YMAGDPTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITE 298 Query: 293 PVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTNGWVVI 352 P+EFSF+FVAP+LY+I++ILAG+ F +C L +R G +FS G ID+++ G S+ W+ Sbjct: 299 PIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFP 358 Query: 353 PVGIVFAFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQN 412 VGI +A +YY +FR I +LKTPGR ED + KA ++A ++ A GG++N Sbjct: 359 IVGIGYAIVYYTIFRVLIKALDLKTPGR---EDATEDAKA-TGTSEMAPALVAAFGGKEN 414 Query: 413 IANLDACITRLRVTVHQPSQVCKDELKRLGAVGVLEVNNNFQAIFGTKSDALKDDI 468 I NLDACITRLRV+V S+V + LK+LGA GV+ + QAIFGTKSD LK ++ Sbjct: 415 ITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEM 470 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: 810 Number of extensions: 46 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: 631 Length of database: 477 Length adjustment: 36 Effective length of query: 595 Effective length of database: 441 Effective search space: 262395 Effective search space used: 262395 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