Align Amino acid transporter (characterized, see rationale)
to candidate CCNA_01242 CCNA_01242 amino acid permease
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__Caulo:CCNA_01242 Length = 531 Score = 320 bits (820), Expect = 8e-92 Identities = 202/518 (38%), Positives = 288/518 (55%), Gaps = 61/518 (11%) Query: 14 RKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGLAGPGVILSFL 72 +K+I +I A S QLK+TL +L++LGVGAI+G GI+ LTG V + AGP ++LSF+ Sbjct: 9 KKSIASIQKEAAHS-QLKRTLGPINLMSLGVGAIIGAGIFVLTGQVASANAGPAIMLSFI 67 Query: 73 IAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVG 132 +AG CA A LCYAEL++ +P SGSAYTY+Y +GE AW +GW L+LEY + + VAVG Sbjct: 68 VAGIACALAGLCYAELASTMPVSGSAYTYAYGTLGEVFAWIMGWLLVLEYGVAASTVAVG 127 Query: 133 WSA------HAHGL-FKMIGFPDA-----------LLAGPHQG------GLINMPAVFIS 168 WS HA G+ F MI A +A P G G +N+ A Sbjct: 128 WSGYVVSTLHALGINFPMIQVAGADAPMWATPLIQAVAAPGGGTMFAMTGTLNLVAAIGI 187 Query: 169 MAVAGLLALGTRESATVNMVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEG 228 V+ LL +G ESA VN +V +K+I L+ F+ + N A++ PF+P P G Sbjct: 188 AMVSALLVVGVSESANVNNAIVVIKVIVLVTFIAVGAQYINPANWHPFIPE------PTG 241 Query: 229 AAADAAKVGVMAAASLIFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVA 288 + G+ A++IFFA+ GF+AVSTAA E KNP RD+ IGI+G++ +CT IYM VA Sbjct: 242 QPGEFGIGGIFRGAAIIFFAYVGFEAVSTAAAEAKNPSRDVPIGILGALIICTLIYMAVA 301 Query: 289 AVSIGASRTEVFSKSEAPLVFILESL------------NHGKIAQL---VALAAVIALPT 333 AV G + S AP+ ++ + GK+ L + + A+ L + Sbjct: 302 AVMTGVVPFRELA-SPAPIAVAIDRMGLEWADIPYAAAEGGKLNLLSFAIKIGAITGLSS 360 Query: 334 VILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIA 393 V+L YGQ+RIF+ MARDGLLP+ ++++ K TP + T+L GV+ A+ + L + + Sbjct: 361 VMLVLCYGQTRIFYTMARDGLLPKVFAEIHPKFRTPWLGTILLGVVIAIAASFLPISLLG 420 Query: 394 ELANAGTLWAFIAVGASVILLRLREPNRPRVFSTPLWPIVAPAGILGCLYL--------- 444 +L + GT AF V SVI LR++ P+ PR F P A AGI CL+L Sbjct: 421 DLVSLGTAVAFSIVCLSVIYLRIKHPDLPRPFKVPGGIFTAAAGIAACLFLPYQNFQPMI 480 Query: 445 ---FLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLAQ 479 P + YA +GA++Y+AYG S LA+ Sbjct: 481 VHAMNDNPLPLMILGGYA-AVGAIIYIAYGYWHSKLAK 517 Lambda K H 0.326 0.138 0.415 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: 726 Number of extensions: 37 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: 483 Length of database: 531 Length adjustment: 34 Effective length of query: 449 Effective length of database: 497 Effective search space: 223153 Effective search space used: 223153 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