Align L-glutamine and L-histidine transporter (characterized)
to candidate WP_102938052.1 B1812_RS04230 amino acid permease
Query= reanno::Korea:Ga0059261_1577 (470 letters) >NCBI__GCF_002117405.1:WP_102938052.1 Length = 481 Score = 313 bits (803), Expect = 6e-90 Identities = 175/465 (37%), Positives = 260/465 (55%), Gaps = 30/465 (6%) Query: 14 AAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGK-AGPAVIMSFVIAGAICA 72 A A E+ L L W L+A+G+G I+G GI L G A AGP V +SF+++G C Sbjct: 20 AENDAEENGLKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPGVTISFLLSGLACT 79 Query: 73 CAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWSGYAAP 132 AL YAE+A ++PA+GS Y Y+Y LGEI AW++GW+L+LEY+ +TVAVGW+GY Sbjct: 80 FVALCYAELAALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGAATVAVGWAGYFNR 139 Query: 133 L-----LHAWTGMPLELMAGPHA----NGIVNLPAIFIIAVVAGLLCLGTKESATLNAAL 183 + +H + A H+ +G+ N+PA II ++ LL GT ES+ N + Sbjct: 140 VMQGLGIHLPEALTSAYFANAHSIGGTHGVFNVPAAAIILLLTALLMRGTSESSFFNNII 199 Query: 184 VVVKIIALAVFVAVALPYFNGANLEPFAP--------FGFAKTISPDGVERGVMAAAAII 235 VV+K++ + V + V + + AN P P FG++ GV+ A+++ Sbjct: 200 VVIKVMVVLVVIFVGAAHVDAANWTPLIPENTDHFGHFGWS----------GVVRGASVV 249 Query: 236 FFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPE 295 FFA+ GFD +STAA+E P RD+ IGI+GS++ C +Y+ VA A G + P+ Sbjct: 250 FFAYIGFDGVSTAAQEAHTPQRDVPIGILGSLVICTILYVAVAAVATGVVSYKEL-GVPD 308 Query: 296 PLALILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSK- 354 P+AL++ G + + + AI L T +L LFGQ+RIF+ MA+DG+LP A V Sbjct: 309 PMALVMDRTGVAWLSWVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGLLPKVFAAVHPV 368 Query: 355 RGSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMF 414 +P VA+ AGL PI+ + + + GTLAAF V ++ LR PDM R F Sbjct: 369 WRTPAVSQALVGVFVALAAGLFPINILDEMVSIGTLAAFALVCGAVLHLRRSQPDMHRPF 428 Query: 415 RTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAY 459 R P + + + C+ L +LP++T L + W A+G+ IYF Y Sbjct: 429 RAPGIPAMPLLGIASCLALMVALPLETWLRLIVWTAIGMAIYFFY 473 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: 635 Number of extensions: 27 Number of successful extensions: 6 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: 481 Length adjustment: 33 Effective length of query: 437 Effective length of database: 448 Effective search space: 195776 Effective search space used: 195776 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: 51 (24.3 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