Align L-glutamine and L-histidine transporter (characterized)
to candidate WP_010959705.1 MCA_RS01690 amino acid permease
Query= reanno::Korea:Ga0059261_1577 (470 letters) >NCBI__GCF_000008325.1:WP_010959705.1 Length = 465 Score = 363 bits (933), Expect = e-105 Identities = 207/459 (45%), Positives = 283/459 (61%), Gaps = 7/459 (1%) Query: 5 LFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAG-KAGPAVIMS 63 +FRTK V + + L L L LG+GAI+GTGI L G+ A +AGPAV++S Sbjct: 3 IFRTKAV--STDDCSGGSLKRCLGALDLTLLGIGAIIGTGIFVLTGIAAATQAGPAVVLS 60 Query: 64 FVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVA 123 FV AG CA AALAYAE+A + GSAY YSYA GE+IAW++GW LILEY++ V+ VA Sbjct: 61 FVFAGLACAFAALAYAELAACVGGCGSAYGYSYAAFGELIAWIIGWDLILEYAISVAAVA 120 Query: 124 VGWSGYAAPLLHA-WTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLNAA 182 GWSGY A L A +P L P GI+NLPA II ++ LL G KESA LN Sbjct: 121 NGWSGYFANALTAVGLELPDYLTKAPEKGGIINLPASAIIILLMALLIAGVKESARLNTV 180 Query: 183 LVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFYGF 242 +V VK++A+AVFVAVA + + A+ +PF PFG+ +G GV+A A+I+FFA+ GF Sbjct: 181 MVSVKVLAIAVFVAVASAHVDPAHWDPFLPFGWFGH-DAEGRPTGVLAGASIVFFAYVGF 239 Query: 243 DAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALILR 302 DA+STAAEE +NP RD+ IGI+GS++ C IY++VA G P+T N P+A L+ Sbjct: 240 DAVSTAAEEARNPMRDVPIGIIGSLVFCTLIYIVVAGLLTGVVPYTEL-NVSSPVAHALQ 298 Query: 303 DLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKR-GSPVRI 361 LG + +A I L TV+L + +RI F M+RDG+L + V+ R +PVR+ Sbjct: 299 LLGIRWASGLVATGVIAGLTTVMLVLYYALTRIIFAMSRDGLLSPWFSAVNTRTQTPVRV 358 Query: 362 TLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWWL 421 + ++++AG +P+ E+A L N GTL AF V + ++VLRV P++ R F+TP+ Sbjct: 359 IVLCGLFISLVAGFVPLGELAELVNIGTLFAFVLVCLGVIVLRVTRPELHRPFKTPVVPW 418 Query: 422 VGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYA 460 + L C L LP T L F+ W LG+ IYFAY+ Sbjct: 419 FPILGALSCGALMAFLPALTWLRFVVWLLLGIGIYFAYS 457 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: 691 Number of extensions: 41 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: 465 Length adjustment: 33 Effective length of query: 437 Effective length of database: 432 Effective search space: 188784 Effective search space used: 188784 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 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