Align L-alanine and D-alanine permease (characterized)
to candidate 1937132 b3795 predicted transporter (NCBI)
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__Keio:1937132 Length = 461 Score = 475 bits (1222), Expect = e-138 Identities = 229/452 (50%), Positives = 327/452 (72%), Gaps = 3/452 (0%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 L+R L RHI L+ALG IGVGLF+G+A ++ AGP+++L+YII GL + IMR++GEM Sbjct: 8 LQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMRSMGEML 67 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137 PV GSF+ YA Y+ P G+LT W+YWF+W+ ++EITA+ VY+ WFP++ +WI Sbjct: 68 FLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPEMAQWIP 127 Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197 AL A+ + NL AV+ +GE EFWFA+IK+ TII M++ G+G+I FGFGN G ++G SN Sbjct: 128 ALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGNGGQSIGFSN 187 Query: 198 LWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257 L HGGF G G L +L +V+ +Y GVE+IG+TAGEAKNPQ T+ +A+G V WRIL+F Sbjct: 188 LTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVLWRILIF 247 Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 YVGA+FVI++I+PWNEIG+ GSPFV+TF ++GI AAGIINFVV+TAALS CN G++S G Sbjct: 248 YVGAIFVIVTIFPWNEIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCNSGMYSCG 307 Query: 318 RMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLV--PEKVFVWVTSIA 375 RMLY+LA+N Q PA AK S +GVP + +SIA LL+G LNY++ P++VFV+V S + Sbjct: 308 RMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYIIPNPQRVFVYVYSAS 367 Query: 376 TFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPD 435 + W +IL++QL+FR++ A+ A+ +R L+P ++Y+ +AFL+ V+ M + D Sbjct: 368 VLPGMVPWFVILISQLRFRRAHKAA-IASHPFRSILFPWANYVTMAFLICVLIGMYFNED 426 Query: 436 TRVALYVGPAFLVLLTVLFYTFKLQPTGDVQR 467 TR++L+VG F++ +T ++ F L G + Sbjct: 427 TRMSLFVGIIFMLAVTAIYKVFGLNRHGKAHK 458 Lambda K H 0.328 0.142 0.444 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: 718 Number of extensions: 36 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: 473 Length of database: 461 Length adjustment: 33 Effective length of query: 440 Effective length of database: 428 Effective search space: 188320 Effective search space used: 188320 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 (21.7 bits) S2: 51 (24.3 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