Align N-acetylglucosamine porter, NagP (characterized)
to candidate 353837 BT4311 glucose/galactose transporter (NCBI ptt file)
Query= TCDB::Q8EBL0 (435 letters) >FitnessBrowser__Btheta:353837 Length = 386 Score = 246 bits (627), Expect = 1e-69 Identities = 153/418 (36%), Positives = 238/418 (56%), Gaps = 40/418 (9%) Query: 21 LFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRKVGYKNG 80 +FF LGFA +N L+P LK L+++ ++ LI+ + +I P+ I+K+GYK Sbjct: 1 MFFSLGFALGINSVLVPVLKGSLEISSAESYLIIAATFIPFLIFGYPAGLTIKKIGYKRT 60 Query: 81 MALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNPYVVRLGPEESAAA 140 M L + IA LFIP+A + F LFL A + G+ LQ AVNPY+ LGP +SAA Sbjct: 61 MVLSFLMFAIAFGLFIPSASYESFPLFLLASFISGSANAYLQAAVNPYITILGPIDSAAK 120 Query: 141 RVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMANGLVLP-YLGMAVFI 199 R+S+MGI NK A I PL + L IG +T + + + L LP Y+ +A FI Sbjct: 121 RISIMGICNKLAWPIPPLFLAFL--------IGKEVTDITVAD----LFLPFYVIIAAFI 168 Query: 200 GILALAVKKSPLPEL-----SNEDEVADHTDKSQIKAAL-SHPNLALGVLALFVYVAVEV 253 L + +PLPE+ + +E A+ + K ++ P+L LG LALF+YV VE Sbjct: 169 A-LGIIAYMAPLPEVKAVGEDDSEEAAEACPYAAKKTSIWQFPHLLLGCLALFLYVGVET 227 Query: 254 IAGDTIGTFALSLGIDHYGVMTSYTMVCMVLGYILGILLIPRVISQPTALMISAILGLLL 313 ++ T+ +A SL +++ + + +V+GYI GI+ IP+ +SQ TAL I ++L + Sbjct: 228 VSLGTLVDYATSLHLENAAMYAWIAPIGIVIGYICGIIFIPKYMSQATALKICSVLAI-- 285 Query: 314 TLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVWPAVWPLALSGMGKLT 373 I ++L+V ++ I+F+ L +++WPA+WPLA++ +GK T Sbjct: 286 -------------IGSVLVVL---TPADISIYFISFMALGCSLMWPALWPLAMADLGKFT 329 Query: 374 STGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLFILFYAVKGHKMRS 431 +GS+LLIM +AGGA P +G + +D+ Q Y + LPC+LFIL+Y V G+K+R+ Sbjct: 330 KSGSSLLIMAMAGGAVIPTLFGYLKDISDI--QKAYWICLPCFLFILYYGVAGYKIRT 385 Lambda K H 0.326 0.141 0.414 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: 524 Number of extensions: 29 Number of successful extensions: 4 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: 435 Length of database: 386 Length adjustment: 31 Effective length of query: 404 Effective length of database: 355 Effective search space: 143420 Effective search space used: 143420 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.9 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