Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= SwissProt::O51924 (295 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 166 bits (420), Expect = 6e-46 Identities = 104/286 (36%), Positives = 154/286 (53%), Gaps = 12/286 (4%) Query: 15 KLGYLMILPLLTVVLVFIILPVMGTFWISLHRDVTF----IPEKPFVGLRNYLRVLSARE 70 + +L + P L V+ +F +LPV+ +SL + I + FV L NY +L Sbjct: 5 RAAWLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELLHRPL 64 Query: 71 FWYSTFVTVSFSFVSVSLETILGLSFALILNERL-KGRGVLRAIVLIPWAVPTIISARTW 129 FW + T+ F V V L + L AL+LN L + + + R + P + A W Sbjct: 65 FWSALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVAVIW 124 Query: 130 ELMYNYSYGLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPFMTLLLLAGLQAIP 189 ++N YGL N+ L LG+ PV+WLG P A I++ VWK + ++ LA LQAIP Sbjct: 125 RYLFNTKYGLANYALGGLGIHPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAALQAIP 184 Query: 190 QDLYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGAT 249 DLYEAA IDGAS +F+ ITLP+L P L++ IL ++F +V+T GGP +T Sbjct: 185 ADLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGGPLQST 244 Query: 250 TSISLL----AFNYYNLGDYGIGSAISILTFVLVLSFTIVYLKVGR 291 TS+ L F ++NLG SA++ L F+++ + T V L+V R Sbjct: 245 TSVLYLMYEEGFKWWNLGS---ASAVAFLLFLIMFAVTAVMLRVAR 287 Lambda K H 0.329 0.145 0.439 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: 283 Number of extensions: 14 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: 295 Length of database: 292 Length adjustment: 26 Effective length of query: 269 Effective length of database: 266 Effective search space: 71554 Effective search space used: 71554 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