Align Large neutral amino acids transporter small subunit 2; L-type amino acid transporter 2; Solute carrier family 7 member 8 (characterized)
to candidate CA265_RS14990 CA265_RS14990 amino acid transporter
Query= SwissProt::Q9WVR6 (533 letters) >FitnessBrowser__Pedo557:CA265_RS14990 Length = 480 Score = 206 bits (525), Expect = 1e-57 Identities = 140/464 (30%), Positives = 233/464 (50%), Gaps = 39/464 (8%) Query: 38 KKEIGLVSACGIIVGNIIGSGIFVSPKGVLENAGSVGLALIVWIVTGVITAVGALCYAEL 97 K+++ L A +++G++IGSGIF+ ++ N GS ++VW++TGV+T A+ Y EL Sbjct: 11 KRKLSLFDATMLVMGSMIGSGIFIVSADIMRNLGSGYWLIVVWVITGVMTVAAAISYGEL 70 Query: 98 GVTIPKSGGDYSYVKDIFGGLAGFLRLWIAVLVIYPTNQAVIALTFSNYV---------L 148 PK+GG Y+Y+K+IFG + GFL W VI A +A+ F + Sbjct: 71 SSMFPKAGGQYTYLKEIFGKMMGFLYGWGLFTVIQTGTIAAVAVAFGKFTAYLIPALNDA 130 Query: 149 QPLFPTCFPPESGLRLLAAICLLLLTWVNCSSVRWATRVQDIFTAGKLLALALIIIMGVV 208 P+F + + +++LA +LLLT++N V +Q+IFT K++AL +II+G Sbjct: 131 APIFQSGGYKITWIQILAIGVILLLTYINTKGVESGKILQNIFTGSKIVALIGLIILGFF 190 Query: 209 QICKGEFFWLE----PKNAFENFQEPD-----------------IGLVALAFLQGSFAYG 247 + FW E +AF N + +G +A A + F+ Sbjct: 191 LVKNS--FWAENLGFGSSAFNNLKTDASGNFLKSGWESISGMTIMGGIAAAMVGSVFSSV 248 Query: 248 GWNFLNYVTEELVDPYKNLPRAIFISIPLVTFVYVFANIAYVTAMSPQEL--LASNAVAV 305 W + +V+ E+ +P KN+ R++ + V +Y+ N Y+ ++ + ++ VAV Sbjct: 249 AWENVTFVSGEIENPKKNVVRSMVLGTSAVMILYLLVNFIYLNTLNRDSIAFALNDRVAV 308 Query: 306 TFGEKLL--GVMAWIMPISVALSTFGGVNGSLFTSSRLFFAGAREGHLPSVLAMIHVKRC 363 E++ G+ ++ + V +STFG VNG + +R+F A++G A+ + K Sbjct: 309 AASEQIFGSGIGTIVIALLVMISTFGCVNGIVLAGARVFQTMAKDGMFFKA-ALKNNKNG 367 Query: 364 TPIPALLFTCLSTLLMLVTSDMYTLINYVGFINYLFYGVTVAGQIVLRWKKPDIPRPIKI 423 P +L + + ++ L++ + F+ LFY +TV G I LR K+P + RP K Sbjct: 368 VPEKSLWMQGIWASALCLSGQYGNLLDMISFVIVLFYMITVFGVIYLRIKQPKLERPYKT 427 Query: 424 SL--LFPIIYLLFWAFLLIFSLWSEPVVCGIGLAIMLTGVPVYF 465 L + PIIYLL A I L + GL I+L GVPVYF Sbjct: 428 WLYPITPIIYLLIGAAFCILLLIYKQQYTWPGLVIVLLGVPVYF 471 Lambda K H 0.325 0.142 0.440 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: 641 Number of extensions: 48 Number of successful extensions: 6 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: 533 Length of database: 480 Length adjustment: 34 Effective length of query: 499 Effective length of database: 446 Effective search space: 222554 Effective search space used: 222554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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