Align L-glutamine and L-histidine transporter (characterized)
to candidate CCNA_01242 CCNA_01242 amino acid permease
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__Caulo:CCNA_01242 Length = 531 Score = 334 bits (857), Expect = 4e-96 Identities = 206/528 (39%), Positives = 289/528 (54%), Gaps = 66/528 (12%) Query: 1 MAGG-LFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIG-VGAGKAGP 58 MAG LF K + ++A +L TL +L++LGVGAI+G GI L G V + AGP Sbjct: 1 MAGNRLFLKKSIASIQKEAAHSQLKRTLGPINLMSLGVGAIIGAGIFVLTGQVASANAGP 60 Query: 59 AVIMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLV 118 A+++SF++AG CA A L YAE+A+ MP SGSAY Y+Y LGE+ AW++GW L+LEY + Sbjct: 61 AIMLSFIVAGIACALAGLCYAELASTMPVSGSAYTYAYGTLGEVFAWIMGWLLVLEYGVA 120 Query: 119 VSTVAVGWSGYAAPLLHA-----------------WTGMPLELMAGPHA------NGIVN 155 STVAVGWSGY LHA W ++ +A P G +N Sbjct: 121 ASTVAVGWSGYVVSTLHALGINFPMIQVAGADAPMWATPLIQAVAAPGGGTMFAMTGTLN 180 Query: 156 LPAIFIIAVVAGLLCLGTKESATLNAALVVVKIIALAVFVAVALPYFNGANLEPF--APF 213 L A IA+V+ LL +G ESA +N A+VV+K+I L F+AV Y N AN PF P Sbjct: 181 LVAAIGIAMVSALLVVGVSESANVNNAIVVIKVIVLVTFIAVGAQYINPANWHPFIPEPT 240 Query: 214 GFAKTISPDGVERGVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAI 273 G G+ RG AAIIFFA+ GF+A+STAA E KNP RD+ IGI+G++I C I Sbjct: 241 GQPGEFGIGGIFRG----AAIIFFAYVGFEAVSTAAAEAKNPSRDVPIGILGALIICTLI 296 Query: 274 YMLVAVAAVGATPFTHFANSPEPLALILRDL--------------GRPGFATF-LAVSAI 318 YM VA G PF A SP P+A+ + + G+ +F + + AI Sbjct: 297 YMAVAAVMTGVVPFRELA-SPAPIAVAIDRMGLEWADIPYAAAEGGKLNLLSFAIKIGAI 355 Query: 319 IALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKV-SKRGSPVRITLFTAAIVAVIAGLLP 377 L +V+L +GQ+RIF+TMARDG+LP A++ K +P T+ ++A+ A LP Sbjct: 356 TGLSSVMLVLCYGQTRIFYTMARDGLLPKVFAEIHPKFRTPWLGTILLGVVIAIAASFLP 415 Query: 378 IDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFS- 436 I + L + GT AF+ V + ++ LR++ PD+PR F+ P A + C++L + Sbjct: 416 ISLLGDLVSLGTAVAFSIVCLSVIYLRIKHPDLPRPFKVPGGIFTAAAGIAACLFLPYQN 475 Query: 437 -------------LPVKTQLWFLAWNALGVVIYFAYARPRVS-AKGIE 470 LP+ + + A+G +IY AY AKGI+ Sbjct: 476 FQPMIVHAMNDNPLPL---MILGGYAAVGAIIYIAYGYWHSKLAKGID 520 Lambda K H 0.327 0.140 0.426 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: 729 Number of extensions: 44 Number of successful extensions: 7 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: 470 Length of database: 531 Length adjustment: 34 Effective length of query: 436 Effective length of database: 497 Effective search space: 216692 Effective search space used: 216692 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