Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >NCBI__GCF_002117405.1:WP_085770386.1 Length = 488 Score = 225 bits (573), Expect = 4e-63 Identities = 132/409 (32%), Positives = 216/409 (52%), Gaps = 24/409 (5%) Query: 24 EESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLC 83 E L R L + LV +G+G +G G++VL G VA AGP + +SFLIA +AS A LC Sbjct: 21 ERGALRRALGLWQLVGIGLGGLIGVGIFVLTGVVAATQAGPGVALSFLIAGVASGAAALC 80 Query: 84 YGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKP 143 Y EF + +P GSAY Y+Y +GEL A+I GW+L+L Y + + V+ WS L+ Sbjct: 81 YAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLEYALVVAVVSIGWSGYLRALLA-- 138 Query: 144 IGEFSRQHMALNAPGVL-AQTPDIFAVIIIIILTGLLTLGVKESAMVNKIFTCINVLVLC 202 + + A APG D+FA++ + LLTL V+ A N + + + Sbjct: 139 LFGVAPPEWAAGAPGTGDGHILDLFAMLGAFGVALLLTLRVEWGARFNTAMVLLKIAAVI 198 Query: 203 FIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATCFYAFVGF 262 ++++ + NW+ FMPFGF GV+ GAA F+A G+ Sbjct: 199 VVILAAAPHINPANWR--------------------PFMPFGFGGVVEGAAVVFFAVFGY 238 Query: 263 DCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLDIDSPLPGAFKH 322 D + T GEE PQ+ +P ++ SL++ Y +S ALT + Y LD +P+ AF Sbjct: 239 DTLTTAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLALTGIARYDTLDNAAPVASAFAA 298 Query: 323 QGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNRTKTPVIAT 382 G A V+ ++ + + +L + R+ +AM+ DGLL + A+ + + TP T Sbjct: 299 LGMGWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSRDGLLPAWFARPHPQFATPYRPT 358 Query: 383 VTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRY-QPEQP 430 + +G + A+++ F ++++ +L++IGTL A+ ++ V+ LR+ +P+ P Sbjct: 359 LIAGGLCALVSAFFPIREVAELVNIGTLSAFVVICLAVIALRHTRPDVP 407 Score = 55.8 bits (133), Expect = 4e-12 Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 2/80 (2%) Query: 525 MTGSVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAV 584 ++ V++C+ V + +P+ F+ P P LP++ + +++L+ +L W RF V Sbjct: 386 LSAFVVICLAVIALRHTRPD--VPRGFRAPLSPYLPLIGVGFSLWLLSKLPAIAWERFVV 443 Query: 585 WMLIGFTIYFGYGIWHSEEA 604 W++IG +YF YG HS A Sbjct: 444 WLIIGLAVYFLYGRRHSRLA 463 Lambda K H 0.324 0.138 0.417 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: 759 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 488 Length adjustment: 36 Effective length of query: 586 Effective length of database: 452 Effective search space: 264872 Effective search space used: 264872 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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