Align LacF, component of Lactose porter (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component
Query= TCDB::P29823 (298 letters) >FitnessBrowser__Phaeo:GFF1647 Length = 316 Score = 134 bits (337), Expect = 3e-36 Identities = 97/293 (33%), Positives = 153/293 (52%), Gaps = 16/293 (5%) Query: 3 TTSRSSLKRYYDVNGWLFVAPAIALISVFMLYPILRSLVLSLYTGRGMMLKFS----GTG 58 T +R SL Y V +L+++P I LI ML P++ + S + ++ F+ G Sbjct: 19 TGARRSLYWQYMVEPFLYLSPMILLIGSVMLIPLIVGISYS-FQSIELLNPFATGWVGFE 77 Query: 59 NLVRLWNDPVFWQALQNTVIFFVVQVPIMITMALILAAMLNNPKLRYSG--LFRTMIFLP 116 N +LW+D FW AL+NT + + + L LA +LN ++ G LF+ ++FLP Sbjct: 78 NYEKLWSDRKFWIALENTFFWTFWSIFFQFFLGLGLAMLLNT---QFFGKKLFQALVFLP 134 Query: 117 CVSSLVAYSILFKSMFS-LDGVVNNTLLAIGIIGEPIGWLTDPFWAKVLIIIAITWRWTG 175 ++ + +F+ + G + + L A+G++ EP L DP A I A W Sbjct: 135 WAVPTFLSALTWAWLFNPVIGPIPHWLAALGVLSEPYNILGDPDLAIWGPITANIWFGVP 194 Query: 176 YNMIFYLAALQNIDRSIYEAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFD 235 + I LAALQ+I +YEAA+IDG W F +T+P L P+I T + TI D Sbjct: 195 FFAITLLAALQSIPGELYEAAEIDGATPWQSFTKITLPFLAPMIAITVMLRTIWIANFAD 254 Query: 236 EVYNFTEGTGGPANSTLTLSLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLSF 288 ++ T GGPANST LS YI+ FR + F YA+T++ + L++ +L++ Sbjct: 255 LIFVMT--GGGPANSTQILSTYIFTTAFRKL-DFGYASTIA--VALLIILLAY 302 Lambda K H 0.329 0.141 0.435 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: 344 Number of extensions: 24 Number of successful extensions: 5 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: 298 Length of database: 316 Length adjustment: 27 Effective length of query: 271 Effective length of database: 289 Effective search space: 78319 Effective search space used: 78319 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 (21.8 bits) S2: 48 (23.1 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