Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate AO356_23210 AO356_23210 ABC transporter
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23210 Length = 340 Score = 130 bits (327), Expect = 5e-35 Identities = 105/327 (32%), Positives = 170/327 (51%), Gaps = 32/327 (9%) Query: 3 KRNLPLMITIGVFVLGYLYCLTQFPGFA--------STRVICNILTDNAFLGIIAVGMTF 54 +R LP ++I + ++G F S R++ IL + +G++A+G+T Sbjct: 17 RRRLPTELSIFLVLIGIGLVFEMFGWIMRDQSFLMNSQRLVLMIL-QVSIIGLLAIGVTQ 75 Query: 55 VILSGGIDLSVGSVIAFTGVFLAKVI--GDFGLS--PLLA-----FPLV--LVMGCAFGA 103 VI++ GIDLS GSV+A + + A + DF + P L P+V L +G GA Sbjct: 76 VIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVVAGLGVGLLAGA 135 Query: 104 FMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLS 163 G +I IP FI TL M RG++ +E P+ ++ S ++ G G Sbjct: 136 INGSIIAITGIPPFIATLGMMVSARGLARYYTE-----GQPV--SMLSDSYTAIGHG--- 185 Query: 164 AMGLLMLAVVVIGIFLAHR-TRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLAT 222 AM +++ VV + +A R T++G YAIGGN +A GI+ + + +Y ++ LA Sbjct: 186 AMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAG 245 Query: 223 LAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYI 282 LAG+V S G A G+ ELDAIA+ VIGGT L+GGVG + GT+ G I G++ + Sbjct: 246 LAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGF 305 Query: 283 NFDGTLSSWWTKIAIGILLFIFIALQR 309 F G + ++ I G+++ + + + + Sbjct: 306 TFVG-VDAYIQDIIKGLIIVVAVVIDQ 331 Lambda K H 0.329 0.145 0.428 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: 28 Number of successful extensions: 3 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: 331 Length of database: 340 Length adjustment: 28 Effective length of query: 303 Effective length of database: 312 Effective search space: 94536 Effective search space used: 94536 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: 49 (23.5 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