Align Amino acid permease-associated region (characterized, see rationale)
to candidate PP_1259 PP_1259 Aspartate-proton symporter
Query= uniprot:B2SZ32 (555 letters) >FitnessBrowser__Putida:PP_1259 Length = 537 Score = 370 bits (951), Expect = e-107 Identities = 197/515 (38%), Positives = 299/515 (58%), Gaps = 14/515 (2%) Query: 25 VKSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPAAVCAWVIGAVVILAIALTY 84 + ++ + L GLG+I GSGWLF A + IAGPA + +W +G +L + + Y Sbjct: 1 MSGKFKKQLSLLDLTFIGLGAIFGSGWLFAASHVSAIAGPAGILSWFLGGFAVLLLGIVY 60 Query: 85 AELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYPWA 144 ELGA P +GG+VRY YSHG L+G++ + IA S+I IE AS QY + W +P Sbjct: 61 CELGAALPRAGGVVRYPVYSHGPLLGYLMGFITLIAFSSLIAIEVVASRQYAAAW-FP-- 117 Query: 145 HALFVDGSL--TTNGLLLSAALVIIYFMLNYWGVKLFARANSAITIFKFLIPGATILGLM 202 L GS T G L+ AL+ ++F LNY VK FA+AN+ +++FKF++P ++G++ Sbjct: 118 -GLTKAGSSDPTVLGWLVQFALLGLFFFLNYRSVKTFAKANNLVSVFKFIVP-LLVIGVL 175 Query: 203 FAGFHKENFGEASTFAPYGWSAVLTAVSTSGIVFAFNGFQSPINLAGEARNPAKSVPFAV 262 F F ENF E FAP+G S V AVS GI+FA+ G I++A E +NP +++P A+ Sbjct: 176 FTFFKPENF-EVQGFAPFGLSGVEMAVSAGGIIFAYLGLTPIISVASEVKNPQRTIPIAL 234 Query: 263 IGSILLALVIYVLLQIAYIGAVNPSDVMKGWSHFN--FASPFAELAIALNLNWLAILLYV 320 I S+LL+ IY LLQ+A++G+V + GW+ A P+ ++A+AL + WLA L+ Sbjct: 235 ILSVLLSTAIYALLQLAFLGSVPTEMLANGWASVTKELALPYRDIALALGVGWLAYLVVA 294 Query: 321 DAFVSPSGTGTTYMATTSRMIYAMERNNTMPKMFGNVHPFYGVPRQAMWFNLLVSFIFLF 380 DA +SPSG G YM T R+IY + T K F + G+PR A+W +S + Sbjct: 295 DAVISPSGCGNIYMNATPRVIYGWAQTGTFFKYFTRIDAESGIPRPALWLTFGLSVFWTL 354 Query: 381 FFRGWSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMKIIAPFAFVCASLI 440 F W +L V+S A V+SY P+S+ ALRR A + RP + GM ++ P +F+ A+LI Sbjct: 355 PFPSWEALINVVSAALVLSYAVAPVSVAALRRNAPHMPRPFRVKGMTVLGPLSFIIAALI 414 Query: 441 LYWAKWPLTGEIILLMVVALPVYFYFQ--AKSGFAGWGRDLKAAWWLVAYLPVMAILSLI 498 +YW+ W ++ L +V +Y + G+ ++++ WL+ + + +LS + Sbjct: 415 VYWSGWNTVSWLLALQIVMFVLYLLCSRFVPTQHLSLGQQVRSSAWLIGFYALTILLSWL 474 Query: 499 GSKQFGGHDLIPYGWDMVVVIAFSLVFYYWGVTSG 533 GS FGG +I + +D VVV A +L YYWG +G Sbjct: 475 GS--FGGLGVIGHPFDTVVVAACALGIYYWGAATG 507 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: 68 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: 537 Length adjustment: 35 Effective length of query: 520 Effective length of database: 502 Effective search space: 261040 Effective search space used: 261040 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