Align Amino acid permease-associated region (characterized, see rationale)
to candidate PfGW456L13_3582 Aspartate-proton symporter
Query= uniprot:B2SZ32 (555 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3582 Length = 548 Score = 372 bits (954), Expect = e-107 Identities = 202/540 (37%), Positives = 311/540 (57%), Gaps = 19/540 (3%) Query: 26 KSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPAAVCAWVIGAVVILAIALTYA 85 + ++ + L GLG+I GSGWLF A + IAGPA + +W++G +L + + Y Sbjct: 4 QGKFKKQLSLIDLTFIGLGAIFGSGWLFAASHVSAIAGPAGIFSWLLGGFAVLLLGIVYC 63 Query: 86 ELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYPWAH 145 ELGA P +GG+VRY YSHG L+G++ + IA S++ IE A+ QY + W +P Sbjct: 64 ELGAALPRAGGVVRYPVYSHGPLLGYLMGFITLIAFSSLVAIEVVAARQYAAAW-FP--- 119 Query: 146 ALFVDGSL--TTNGLLLSAALVIIYFMLNYWGVKLFARANSAITIFKFLIPGATILGLMF 203 AL GS T G L+ L+ ++FMLNY+ VK FA+AN+ I++FKF++P ++G++F Sbjct: 120 ALTQAGSSNPTAIGWLVQFGLLCLFFMLNYYSVKTFAKANNLISMFKFIVP-LLVIGVLF 178 Query: 204 AGFHKENFGEASTFAPYGWSAVLTAVSTSGIVFAFNGFQSPINLAGEARNPAKSVPFAVI 263 F ENF ++ F P+G S V AVS GI+FA+ G I++A E +NP +++P A+I Sbjct: 179 TFFKPENF-QSQGFMPFGLSGVEMAVSAGGIIFAYLGLTPIISVASEVKNPQRTIPIALI 237 Query: 264 GSILLALVIYVLLQIAYIGAVNPSDVMKGWSHF--NFASPFAELAIALNLNWLAILLYVD 321 S+LL+ IYVLLQ+A++G V + GW+ A P+ ++A+AL + WLA L+ D Sbjct: 238 LSVLLSTAIYVLLQVAFLGGVPTEMLANGWAGVAKELALPYRDIALALGVGWLAYLVVAD 297 Query: 322 AFVSPSGTGTTYMATTSRMIYAMERNNTMPKMFGNVHPFYGVPRQAMWFNLLVSFIFLFF 381 A +SPSG G YM T R+IY + T K+F + G+PR A+W +S + Sbjct: 298 AVISPSGCGNIYMNATPRVIYGWAQTGTFFKVFTRIDEKSGIPRPALWLTFALSVFWTLP 357 Query: 382 FRGWSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMKIIAPFAFVCASLIL 441 F W +L V+S A V+SY P+S+ ALRR A D+ RP + M ++ P +F+ A+LI+ Sbjct: 358 FPSWEALINVVSAALVLSYAVAPVSVAALRRNAPDMPRPFKVKRMGVLGPVSFIIAALIV 417 Query: 442 YWAKWPLTGEIILLMVVALPVYFYFQ--AKSGFAGWGRDLKAAWWLVAYLPVMAILSLIG 499 YW+ W ++ L ++ VY + + ++++ WL+ + V +LS +G Sbjct: 418 YWSGWSTVSWLLGLQILMFVVYLLCGRFVPTQHLSLAQQVRSSAWLIGFYAVTIVLSWLG 477 Query: 500 SKQFGGHDLIPYGWDMVVVIAFSLVFYYWGVTSG-----YRSEYLDERSEHDEVLEGMGA 554 S FGG ++ + +D VVV A ++ YYWG +G R E D S+ D V G A Sbjct: 478 S--FGGMGVLTHPFDTVVVAACAMGIYYWGAATGVPAHLVRLEDEDGESQADPVHTGTTA 535 Lambda K H 0.326 0.139 0.445 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: 1042 Number of extensions: 67 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: 555 Length of database: 548 Length adjustment: 36 Effective length of query: 519 Effective length of database: 512 Effective search space: 265728 Effective search space used: 265728 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: 53 (25.0 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