Align Amino acid permease-associated region (characterized, see rationale)
to candidate RR42_RS36375 RR42_RS36375 aspartate:proton symporter
Query= uniprot:B2SZ32 (555 letters) >FitnessBrowser__Cup4G11:RR42_RS36375 Length = 524 Score = 363 bits (931), Expect = e-104 Identities = 193/529 (36%), Positives = 302/529 (57%), Gaps = 14/529 (2%) Query: 25 VKSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPAAVCAWVIGAVVILAIALTY 84 V+ +R + L GLG+I GSGWLF A + IAGPA + +W++G +L + + Y Sbjct: 4 VQGKFKRQLSLTDLTFIGLGAIFGSGWLFAASHVSAIAGPAGIISWLLGGFAVLLLGIVY 63 Query: 85 AELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYPWA 144 ELGA P +GG++RY +SHG L+G++ IA S+I IE A+ QY + W +P+ Sbjct: 64 CELGAALPRAGGIIRYPVFSHGELMGYLMGLITLIAFSSLIAIEVVAARQYAAAW-FPF- 121 Query: 145 HALFVDGSL--TTNGLLLSAALVIIYFMLNYWGVKLFARANSAITIFKFLIPGATILGLM 202 L GS T G L A++ ++F+LNY+ VK FARAN+ +++FKF++P I+ ++ Sbjct: 122 --LSQPGSSNPTLPGWALQFAMLCLFFVLNYYSVKTFARANNIVSVFKFVVPLLVIV-VL 178 Query: 203 FAGFHKENFGEASTFAPYGWSAVLTAVSTSGIVFAFNGFQSPINLAGEARNPAKSVPFAV 262 F F N + FAP+G S + AVS GI+FA+ G I++A E R+P +++P A+ Sbjct: 179 FTHFKPANL-QVHGFAPFGLSGIQAAVSAGGIIFAYLGLTPIISVASEVRSPQRTIPIAL 237 Query: 263 IGSILLALVIYVLLQIAYIGAVNPSDVMKGWSHFN--FASPFAELAIALNLNWLAILLYV 320 I S+LL+ +IYVLLQIA++G V + GW FA P+ ++A+AL + WLA L+ Sbjct: 238 ILSVLLSTLIYVLLQIAFLGGVPTETLSDGWRGVGQAFALPYRDIALALGVGWLAFLVVS 297 Query: 321 DAFVSPSGTGTTYMATTSRMIYAMERNNTMPKMFGNVHPFYGVPRQAMWFNLLVSFIFLF 380 DA +SPSGTG YM T R++Y R T K F + G+PR A+W +S + Sbjct: 298 DAVISPSGTGNIYMNATPRVVYGWARGGTFFKSFSRIDAASGIPRPALWLTFALSVFWTL 357 Query: 381 FFRGWSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMKIIAPFAFVCASLI 440 F W ++ V+S A V+SY P+++ ALRR A L RP + + ++ P +F+ A+LI Sbjct: 358 PFPSWEAMINVVSAALVLSYAVAPVTVAALRRNAPSLHRPFRVRWLAVLGPLSFIIAALI 417 Query: 441 LYWAKWPLTGEIILLMVVALPVYFYFQ--AKSGFAGWGRDLKAAWWLVAYLPVMAILSLI 498 +YW+ W ++ L + VY + + + +K++ WL+A+ ++ + S + Sbjct: 418 VYWSGWGTVSWLLGLQIAMFVVYLLCRRAVPTHRLSLAQQVKSSLWLIAFYLLIIVASYL 477 Query: 499 GSKQFGGHDLIPYGWDMVVVIAFSLVFYYWGVTSGYRSEYLDERSEHDE 547 G+ FGG I + WD +V +L Y WG +G + LD + DE Sbjct: 478 GT--FGGIGAISHPWDTGLVALIALGIYGWGARTGIPAALLDLGGDDDE 524 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: 1027 Number of extensions: 60 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: 555 Length of database: 524 Length adjustment: 35 Effective length of query: 520 Effective length of database: 489 Effective search space: 254280 Effective search space used: 254280 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