Align Monocarboxylate 2-oxoacid-binding periplasmic protein all3028; Extracellular solute-binding protein; Extracytoplasmic solute receptor protein all3028; TRAP transporter monocarboxylate 2-oxoacid-binding subunit P (characterized)
to candidate AZOBR_RS14605 AZOBR_RS14605 ABC transporter substrate-binding protein
Query= SwissProt::Q8YSQ6 (364 letters) >FitnessBrowser__azobra:AZOBR_RS14605 Length = 368 Score = 374 bits (961), Expect = e-108 Identities = 180/365 (49%), Positives = 250/365 (68%), Gaps = 3/365 (0%) Query: 1 MKRREVLNTA-AIATATTALVSCTQTNTSSVQAGLPNVRWRMTTSWPKSLGTFIGA-ETV 58 +KRR L +A A A A A ++ ++ P ++WR+ +S+PKS GA E + Sbjct: 1 VKRRAFLKSAGAGAAAAGAGLAVAGVAAPAIAQSQPEIQWRLASSFPKSTDILFGASELI 60 Query: 59 AKRVAEMTNGRFKITPFAAGELVPGLQVLDAVQAGTVECGHTSSYYYIGKSPALAFATSV 118 A+RVAE T+G+F+I F GELVPGLQVLDAVQ G+V+CGHT YYY+GK P AF T++ Sbjct: 61 ARRVAESTDGKFQIRAFPGGELVPGLQVLDAVQNGSVQCGHTCGYYYVGKDPTFAFDTAI 120 Query: 119 PFGLNAQQQYAWLYQGGGLAAIQKIYANFNVINFPAGSTGAQMGGWFKKEIKSVSDLKGL 178 PFG NA+Q AW +Q GGL ++ N NVI FPAG+TGAQMGGW++KEIK+ +D +GL Sbjct: 121 PFGPNARQTTAW-FQAGGLDLMRAFMKNHNVIQFPAGNTGAQMGGWYRKEIKTAADFQGL 179 Query: 179 KMRIPGLGGQVMSRLGVNVQVLPGGEIYLALDRGAIDAAEWVGPYDDEKLGLNKAAQFYY 238 K+RI G+ GQ+MS++G + G ++Y AL++G IDA E+VGPYDDE+LG ++ A++YY Sbjct: 180 KIRIAGITGQIMSKMGATPTQIAGADVYPALEKGTIDATEFVGPYDDERLGFHQVAKYYY 239 Query: 239 YPGWWEPGPTLDVLVNLNAWNRLPKEYQEIFKTATVEANLTMLNQYDALNGEALTRLLAG 298 YPGWWE GP + + VNL W +LPK YQ I A EAN M+ +YD+ N +AL RL+A Sbjct: 240 YPGWWEGGPNVSLYVNLQEWEKLPKSYQSILTAACAEANTYMIARYDSENAKALKRLVAK 299 Query: 299 GTKLVPYSQEIMQAAQKISFDIFEENASKDAAFKQVYEQWKAFRKQIFAWNRVNELSYEN 358 GT L Y +++M+ A KI+F+ ++E A + FK +YE WK F + W RV EL Y++ Sbjct: 300 GTLLRAYPRDLMEQAHKIAFEYYDELAKTNPNFKTIYESWKPFLDETQLWFRVAELPYDS 359 Query: 359 FASSS 363 F +S+ Sbjct: 360 FVASA 364 Lambda K H 0.317 0.132 0.397 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: 455 Number of extensions: 18 Number of successful extensions: 3 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: 364 Length of database: 368 Length adjustment: 30 Effective length of query: 334 Effective length of database: 338 Effective search space: 112892 Effective search space used: 112892 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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