Align Amino acid permease-associated region (characterized, see rationale)
to candidate GFF2803 PS417_14300 aspartate:proton symporter
Query= uniprot:B2SZ32 (555 letters) >FitnessBrowser__WCS417:GFF2803 Length = 539 Score = 367 bits (942), Expect = e-106 Identities = 192/526 (36%), Positives = 301/526 (57%), Gaps = 10/526 (1%) Query: 26 KSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPAAVCAWVIGAVVILAIALTYA 85 + ++ + L GLG+I GSGWLF A + IAGPA + +W+IG +L + + Y Sbjct: 4 QGKFKKQLSLMDLTFIGLGAIFGSGWLFAASHVSAIAGPAGIISWLIGGFAVLLLGIVYC 63 Query: 86 ELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYPWAH 145 ELGA P +GG+VRY YSHG L+G++ + IA S++ IE AS QY + W Sbjct: 64 ELGAALPRAGGVVRYPVYSHGPLLGYLMGFITLIAFSSLVAIEVVASRQYAAAWFPELTK 123 Query: 146 ALFVDGSLTTNGLLLSAALVIIYFMLNYWGVKLFARANSAITIFKFLIPGATILGLMFAG 205 A D TT G L+ AL+ ++F+LNY VK FA AN+ +++FKF++P ++G++F Sbjct: 124 AGSSDP--TTLGWLVQFALLCLFFVLNYRSVKTFAIANNLVSVFKFIVP-LLVIGVLFTF 180 Query: 206 FHKENFGEASTFAPYGWSAVLTAVSTSGIVFAFNGFQSPINLAGEARNPAKSVPFAVIGS 265 F NF + FAP+G S + AVS G++FA+ G I++A E +NP +++P A+I S Sbjct: 181 FKPANF-QVQGFAPFGLSGIEMAVSAGGVIFAYLGLTPIISVASEVKNPQRTIPIALILS 239 Query: 266 ILLALVIYVLLQIAYIGAVNPSDVMKGWSHFN--FASPFAELAIALNLNWLAILLYVDAF 323 +LL+ IYVLLQ A++G V + GW+ + A P+ ++A+AL + WLA L+ DA Sbjct: 240 VLLSTAIYVLLQTAFLGGVPTEMLANGWAGISKELALPYRDIALALGVGWLAYLVVADAV 299 Query: 324 VSPSGTGTTYMATTSRMIYAMERNNTMPKMFGNVHPFYGVPRQAMWFNLLVSFIFLFFFR 383 +SPSG G YM T R++Y + T K+F + G+PR A+W +S + F Sbjct: 300 ISPSGCGNIYMNATPRVVYGWAQTGTFFKIFTRIDEKSGIPRPALWLTFALSVFWTLPFP 359 Query: 384 GWSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMKIIAPFAFVCASLILYW 443 W +L V+S A ++SY P+++ ALRR A + RP + GM ++ P +F+ A+LI+YW Sbjct: 360 SWEALINVVSAALILSYAVAPVTVAALRRNAPQMARPFRVKGMAVLGPLSFIIAALIVYW 419 Query: 444 AKWPLTGEIILLMVVALPVYFYFQ--AKSGFAGWGRDLKAAWWLVAYLPVMAILSLIGSK 501 + W ++ L ++ VY + + ++++ WL+ + V +LS +GS Sbjct: 420 SGWNTVSWLLGLQILMFVVYLLCARWVPTAHLNIKQQVRSSAWLIGFYAVTILLSKLGS- 478 Query: 502 QFGGHDLIPYGWDMVVVIAFSLVFYYWGVTSGYRSEYLDERSEHDE 547 FGG +I + D +VV A +L YYWG +G + + E DE Sbjct: 479 -FGGIGVIGHPLDTIVVAACALGIYYWGAATGVPAHLVRLEHEADE 523 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: 1002 Number of extensions: 61 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: 539 Length adjustment: 36 Effective length of query: 519 Effective length of database: 503 Effective search space: 261057 Effective search space used: 261057 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 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