Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate 14712 b0576 phenylalanine transporter (NCBI)
Query= TCDB::M1IW84 (556 letters) >FitnessBrowser__Keio:14712 Length = 458 Score = 327 bits (839), Expect = 5e-94 Identities = 174/454 (38%), Positives = 269/454 (59%), Gaps = 11/454 (2%) Query: 11 TDTQPHLRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIGFFVFFVLR 70 ++ +P L R L NRHIQLIA+GGAIGTGLF+G G I +AGPAV++ YG+ G F ++R Sbjct: 13 SNQEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMR 72 Query: 71 AMGELLLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPG 130 +GE+++ SF FA GP AGF GW+YW +V+ G+A+L A Y ++W+P Sbjct: 73 QLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPD 132 Query: 131 LPIWVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHG 190 +P W+ A +I AVNL +VR +GE EFWFALIKV AI+ +I G L+ F G Sbjct: 133 VPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLL---FSGHGG 189 Query: 191 VHATIENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAV 250 A+I+NLW GFF TG+ G++ + F++ G+EL+G AAE DP +++P+A+N V Sbjct: 190 EKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQV 249 Query: 251 PLRVAVFYIGALLAILAVVPWRQFASGESPFVTMFSLAGLAAAASVVNFVVVTAAASSAN 310 R+ +FYIG+L+ +LA+ PW + S SPFV +F AS +NFV++ A+ S N Sbjct: 250 VYRILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYN 309 Query: 311 SGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRSVIGAF 370 SG +S RMLFGL+ +G+AP +++R GVP +L+L+ +TS+ +L AF Sbjct: 310 SGVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSG--AITSLVVLINYLLPQKAF 367 Query: 371 TLVTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTDSVYK---MPGGVVMCWAVLVFFAFV 427 L+ + + W MI +++L +R ++ ++ +K P G +C + F + Sbjct: 368 GLLMALVVATLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLC---IAFLGMI 424 Query: 428 IWTLTTETETATALAWFPLWFVLLAVGWLVTQRR 461 + + T + + P+W V L + + +R+ Sbjct: 425 LLLMCTMDDMRLSAILLPVWIVFLFMAFKTLRRK 458 Lambda K H 0.328 0.140 0.442 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: 644 Number of extensions: 36 Number of successful extensions: 2 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: 556 Length of database: 458 Length adjustment: 34 Effective length of query: 522 Effective length of database: 424 Effective search space: 221328 Effective search space used: 221328 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: 52 (24.6 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