Align Branched chain amino acid transporter 2 of 439 aas and 12 TMSs, BrnQ (characterized)
to candidate PP_4184 PP_4184 branched chain amino acid transporter
Query= TCDB::P0AD99 (439 letters) >FitnessBrowser__Putida:PP_4184 Length = 437 Score = 588 bits (1517), Expect = e-173 Identities = 291/428 (67%), Positives = 353/428 (82%) Query: 5 LRSRDIIALGFMTFALFVGAGNIIFPPMVGLQAGEHVWTAAFGFLITAVGLPVLTVVALA 64 L+ +DI+ALGFMTFALFVGAGNIIFPP+VGLQ+G HVW AA GFL+TAVGLPV+TVVALA Sbjct: 4 LKGQDILALGFMTFALFVGAGNIIFPPIVGLQSGPHVWMAALGFLVTAVGLPVITVVALA 63 Query: 65 KVGGGVDSLSTPIGKVAGVLLATVCYLAVGPLFATPRTATVSFEVGIAPLTGDSALPLFI 124 KVGGG+D+LS+PIGK G LLA VCYL+VGPLFATPRTATVSFEVG+APLTG+S L LFI Sbjct: 64 KVGGGMDALSSPIGKFFGGLLAAVCYLSVGPLFATPRTATVSFEVGVAPLTGESPLALFI 123 Query: 125 YSLVYFAIVILVSLYPGKLLDTVGNFLAPLKIIALVILSVAAIVWPAGSISTATEAYQNA 184 YSLVYF +V+ VS+YPGKLLDTVG FLAPLKIIAL +L +AA PAGSI A AY A Sbjct: 124 YSLVYFIVVLAVSMYPGKLLDTVGRFLAPLKIIALAVLGIAAFALPAGSIGDAQPAYAAA 183 Query: 185 AFSNGFVNGYLTMDTLGAMVFGIVIVNAARSRGVTEARLLTRYTVWAGLMAGVGLTLLYL 244 AFS GF +GYLTMDTLGA+VFGIVIVNA RSRGV RL+TRY + AGL+AGVGL L+Y+ Sbjct: 184 AFSKGFSDGYLTMDTLGALVFGIVIVNAIRSRGVESPRLITRYAIIAGLIAGVGLALVYI 243 Query: 245 ALFRLGSDSASLVDQSANGAAILHAYVQHTFGGGGSFLLAALIFIACLVTAVGLTCACAE 304 +LFRLG+ S + + NGAA+LHAYVQHTFG GS LA LI +ACLVTAVGLTCACAE Sbjct: 244 SLFRLGATSHDIAADATNGAAVLHAYVQHTFGSLGSGFLAVLIALACLVTAVGLTCACAE 303 Query: 305 FFAQYVPLSYRTLVFILGGFSMVVSNLGLSQLIQISVPVLTAIYPPCIALVVLSFTRSWW 364 +F+Q +PLSYR LV IL GFS+++SNLGL++LI S+PVLTAIYPPCI +V LSF + W Sbjct: 304 YFSQILPLSYRALVVILAGFSLLISNLGLTKLIMFSIPVLTAIYPPCIVVVGLSFVKDLW 363 Query: 365 HNSSRVIAPPMFISLLFGILDGIKASAFSDILPSWAQRLPLAEQGLAWLMPTVVMVVLAI 424 ++ +R++AP M +SLLFG++D IK S+ + +LP + LPL++ G+AWL+P+VV +V A+ Sbjct: 364 NSPTRILAPVMLVSLLFGMVDAIKGSSLAHVLPDFMAHLPLSDAGMAWLVPSVVTLVGAV 423 Query: 425 IWDRAAGR 432 DR G+ Sbjct: 424 ACDRMLGK 431 Lambda K H 0.327 0.140 0.424 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: 696 Number of extensions: 20 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: 439 Length of database: 437 Length adjustment: 32 Effective length of query: 407 Effective length of database: 405 Effective search space: 164835 Effective search space used: 164835 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