Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_086509707.1 BZY95_RS09540 ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_002151265.1:WP_086509707.1 Length = 540 Score = 175 bits (443), Expect = 3e-48 Identities = 102/251 (40%), Positives = 149/251 (59%), Gaps = 10/251 (3%) Query: 1 MIEFHDVHKTYRVAG------REIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRL 54 ++E +++K +R G RE+ AL + G+ G++G SG+GKSTL R + RL Sbjct: 278 LLEVRNLNKVFRSRGGLFKPAREVRALDDVSFTLAPGETVGIVGESGSGKSTLGRCVVRL 337 Query: 55 EEPSGGRILVEGEDVTALDAEGLRRFRQRVGMIFQ--HFNLLSSKTVADNIAMPLRLAGG 112 E P G + + G D +AL + LRR R+RV MIFQ + +L V IA +A G Sbjct: 338 ERPDSGSLSLSGTDFSALKGDELRRERRRVQMIFQDPYASLNPRHRVGYAIAQG-PMANG 396 Query: 113 FSRAEVDARVSELLARVGLSDHA-RKYPAQLSGGQKQRVGIARALACRPSILLCDEATSA 171 R + + ELL VGL A +YP + SGGQ+QR+GIARALA P +++ DEA SA Sbjct: 397 VPRRQAMQQAEELLELVGLGAVAVDRYPHEFSGGQRQRIGIARALALNPELIVADEAVSA 456 Query: 172 LDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFL 231 LD A VL+LL E+ ++L L+++ ITH++ V ++CD + VM G IVEQG +VFL Sbjct: 457 LDVSIQAQVLELLEELKQKLSLSLLFITHDLRVAAQICDSIIVMQHGRIVEQGTAQEVFL 516 Query: 232 HPQHPTTRRFV 242 P+ T++ + Sbjct: 517 RPREAYTKQLL 527 Score = 130 bits (328), Expect = 6e-35 Identities = 81/230 (35%), Positives = 127/230 (55%), Gaps = 10/230 (4%) Query: 20 ALQPTRLNIQAGQIFGLIGHSGAGKS----TLLRLINRLEEPSGGRILVEGEDVTALDAE 75 A++ ++ G+I ++G SG+GKS ++ L+ + P+ G +L +G+++ AL+ + Sbjct: 26 AVEEVSYDVARGEIMCVVGESGSGKSMAANAVMGLLPKGVRPTAGEVLFDGQNLLALNEK 85 Query: 76 GLRRFRQ-RVGMIFQH--FNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLS 132 R+ R R+GMIFQ L V IA G +S E + LL VG+ Sbjct: 86 QHRKLRGLRIGMIFQEPMTALNPLMRVGAQIAEVFEAHGKYSSRERQEKALALLEEVGIP 145 Query: 133 DH---ARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINR 189 + R YP QLSGGQ+QRV IA ALA P +L+ DE T+ALD T A +L+L+ ++ + Sbjct: 146 EPDKAIRAYPFQLSGGQRQRVMIAMALALEPELLIADEPTTALDVTTQAQILELIRDLQQ 205 Query: 190 ELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTR 239 + ++ ITH+ V+ V +V VM G +VE G +V +P+H TR Sbjct: 206 RRGMAVMFITHDFGVVAEVATRVCVMRYGRVVELGTAREVLENPRHEYTR 255 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: 439 Number of extensions: 23 Number of successful extensions: 4 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: 540 Length adjustment: 32 Effective length of query: 303 Effective length of database: 508 Effective search space: 153924 Effective search space used: 153924 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 24 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