Align Amino acid transporter (characterized, see rationale)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease
Query= uniprot:A0A0H3C3Q5 (483 letters) >NCBI__GCF_900115975.1:WP_092483642.1 Length = 484 Score = 348 bits (894), Expect = e-100 Identities = 190/478 (39%), Positives = 281/478 (58%), Gaps = 18/478 (3%) Query: 8 VSFWTRRKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAG-LAGPG 66 +S W ++ + + L TL L ALGVGA++GTGI+ LTGV A AGPG Sbjct: 1 MSVWRKKPVEQVLADKKKNKRGLVPTLGVADLTALGVGAVIGTGIFVLTGVAAANYAGPG 60 Query: 67 VILSFLIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVC 126 V+ SF+++G AA+ YAEL IP++GSAYT+SY ++GE +AW VGW+LILEY + Sbjct: 61 VVFSFILSGIAATLAAMVYAELGAAIPSAGSAYTFSYVSLGEIIAWLVGWNLILEYLVAA 120 Query: 127 AAVAVGWSAHAHGLFKMIGF--PDALLAGPHQGGLINMPAVFISMAVAGLLALGTRESAT 184 AV++GWS++ L + +G P A + P GG++N+PA I + + GL+ GT+ S T Sbjct: 121 GAVSIGWSSYMGDLLQSVGITLPAAFTSSPFDGGIVNLPAALIVLVITGLIITGTQHSTT 180 Query: 185 VNMVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASL 244 N ++V K+ A+ +F+ L + N A++ P +P G GV A++ Sbjct: 181 ANKIIVVAKLAAIALFIALGVQHINPANWRPVLPYGIS--------------GVFHGAAI 226 Query: 245 IFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSE 304 +FFA+ GFDAV+TA+EE KNP+RDL GI+ ++ + T +Y++VA + G + + + Sbjct: 227 VFFAYIGFDAVATASEEVKNPQRDLPRGIIWTLVISTLLYIVVAGILTGMVKYTNLNTA- 285 Query: 305 APLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNA 364 +P+ L + LV++ A+ L +V+L MYGQSRIFF MARD LLP ++ Sbjct: 286 SPVATALLRAGIPWASALVSVGALAGLTSVLLVAMYGQSRIFFAMARDDLLPPIFDWLHP 345 Query: 365 KTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRV 424 + TPV +++ GVL A+I L + +AELAN GTL AFIAV I+LR P+ R Sbjct: 346 RLRTPVWDSIIIGVLVALIGAFLPIGLVAELANIGTLTAFIAVSTGAIILRRTNPDLRRP 405 Query: 425 FSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLAQQER 482 F P P + I+ YL ++LP T + F+ IG VVY YG RKS LA++ + Sbjct: 406 FRLPWMPAIPVLTIISAGYLAINLPPLTWVRFIAWVAIGLVVYWLYGYRKSKLARESQ 463 Lambda K H 0.326 0.138 0.415 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: 667 Number of extensions: 38 Number of successful extensions: 5 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: 483 Length of database: 484 Length adjustment: 34 Effective length of query: 449 Effective length of database: 450 Effective search space: 202050 Effective search space used: 202050 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: 52 (24.6 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