Align N-acetylglucosamine porter, NagP (characterized)
to candidate 6936095 Sama_0292 glucose/galactose transporter (RefSeq)
Query= TCDB::Q8EBL0 (435 letters) >FitnessBrowser__SB2B:6936095 Length = 389 Score = 185 bits (469), Expect = 2e-51 Identities = 138/420 (32%), Positives = 212/420 (50%), Gaps = 52/420 (12%) Query: 18 VAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRKVGY 77 + LFFI GF T LN L+P+LK +L+ QA L+ F F+ A + + +I K+GY Sbjct: 1 MTTLFFIWGFITALNDILIPHLKAAFELSYTQAMLVQFCFFGAYFIVSPFAGKLIEKIGY 60 Query: 78 KNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNPYVVRLGPEES 137 G+ G+ M LLF PAA+ V+ALFL V+ +G T+LQ + NPYV LG E + Sbjct: 61 IRGIVTGLCTMATGCLLFYPAAEVSVYALFLLGLFVLASGITILQVSANPYVAILGAERT 120 Query: 138 AAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMANGLVLPYLGMAV 197 AA+R+S+ +N +APL +ALI + + A+ + LPYL +A Sbjct: 121 AASRLSLAQAINSLGHTLAPLFGAALIFGAASN--------------AHAVQLPYLILAG 166 Query: 198 FIGILALAVKKSPLPELSNEDEVADHTDKSQIKAALSHPNLALGVLALFVYVAVEVIAGD 257 + + A+ LP L + E T S + H +L LG LA+F+YV EV G Sbjct: 167 AVLLTAVGFVFLKLPTLQTDHE----TQVSHSDSIWQHKHLVLGALAIFLYVGAEVSVGS 222 Query: 258 TIGTF-----ALSLGIDHYGVMTSY----TMVCMVLGYILGILLIPRVISQPTALMISAI 308 + + +L M SY MV +G L +L P + ALM AI Sbjct: 223 FLVNYFSESHIAALSEQEASRMVSYYWGGAMVGRFVGSALTRILQPTYVLATNALM--AI 280 Query: 309 LGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVWPAVWPLALSG 368 L L+LT+ N+S A+A + + +G N+I++P ++ LA+ G Sbjct: 281 LLLVLTM------NSSGALA---------------MWSVLAVGFFNSIMFPTIFTLAIRG 319 Query: 369 MGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLFILFYAVKGHK 428 +G LTS GS LL I GGA P+ G+++ ++ + Q +++ + YL+I +YA++G K Sbjct: 320 LGPLTSRGSGLLCQAIVGGAILPLLQGVVADSSSV--QFSFVIPMVAYLYIGWYALRGSK 377 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: 458 Number of extensions: 25 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: 389 Length adjustment: 31 Effective length of query: 404 Effective length of database: 358 Effective search space: 144632 Effective search space used: 144632 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