Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate AZOBR_RS30440 AZOBR_RS30440 hypothetical protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__azobra:AZOBR_RS30440 Length = 682 Score = 168 bits (426), Expect = 3e-46 Identities = 96/236 (40%), Positives = 139/236 (58%), Gaps = 3/236 (1%) Query: 20 ALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGLRR 79 A+ IQ G++ G++G SG+GKST+ R + L EP+ G +L +G D EG R Sbjct: 372 AVDDVSFTIQRGEVLGVVGESGSGKSTIGRSLLALIEPTAGTVLFDGADFVKQAKEGNRD 431 Query: 80 FRQRVGMIFQHF--NLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGL-SDHAR 136 R+R ++FQ+ +L KTV + PL LAG AE ++ LL RVGL + +A Sbjct: 432 LRRRAQLVFQNSAASLNPRKTVGAAMERPLVLAGRQGEAERREMIAALLTRVGLPAAYAD 491 Query: 137 KYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIV 196 +YP +LSGG++QRV IARALA P ++CDEA SALD A++L LLA++ EL L+ + Sbjct: 492 RYPHELSGGERQRVNIARALATDPEFVVCDEAVSALDVSVQANILNLLADLRDELGLSYL 551 Query: 197 LITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAERVDEDE 252 ITH++ V+ + D+V V+ GG I E+G + V P HP T + R+ E Sbjct: 552 FITHDIAVVSHIADRVLVVYGGTICEEGPIGRVLRPPYHPYTEALLSAVPRLSGAE 607 Score = 162 bits (409), Expect = 3e-44 Identities = 102/288 (35%), Positives = 152/288 (52%), Gaps = 12/288 (4%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKST----LLRLINRLEE 56 ++E ++ Y + A I+ G++ GL+G SG+GKST +L L+ Sbjct: 1 LLEVRNLTINYASPRGTLRAASDVSFAIRPGEVMGLVGESGSGKSTVAMAILDLLGEAGR 60 Query: 57 PSGGRILVEGEDVTALDAEGLRRFR-QRVGMIFQH--FNLLSSKTVADNIAMPLRLAGGF 113 GG IL EG D+ L A R R R+ +FQ +L + TV IA PL GF Sbjct: 61 IDGGEILFEGTDLRRLSAAHRRSLRGDRIAAVFQDPFTSLNPALTVGRQIAEPLVQHKGF 120 Query: 114 SRAEVDARVSELLARVGLSDH---ARKYPAQLSGGQKQRVGIARALACRPSILLCDEATS 170 + + RV ELLA VG+ + A+ YP QLSGG +QRV IA AL C P +L+ DE T+ Sbjct: 121 TPRQAAPRVEELLAEVGIREPRRIAQSYPHQLSGGMQQRVLIATALGCDPKLLILDEPTT 180 Query: 171 ALDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVF 230 ALD A +++LLA + L+ + ++H + ++ R+C+ V V+ G +VE G DV Sbjct: 181 ALDVTVEARIIELLAGLCESHHLSALFVSHNLGIVNRICNSVCVLYGSEVVETGRTRDVL 240 Query: 231 LHPQHPTTRRFVFEAERVDEDERHDDFAHVPGLILRLTFRGEA-TYAP 277 P HP T+ V R+ D RH + +PG + +L+ E+ +AP Sbjct: 241 ARPVHPYTKGLVAALPRITTDRRH-RLSSIPGTVSKLSGASESCVFAP 287 Lambda K H 0.322 0.138 0.393 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: 597 Number of extensions: 27 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 335 Length of database: 682 Length adjustment: 33 Effective length of query: 302 Effective length of database: 649 Effective search space: 195998 Effective search space used: 195998 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 51 (24.3 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