Align histidine permease (characterized)
to candidate WP_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >NCBI__GCF_002095475.1:WP_084934657.1 Length = 463 Score = 375 bits (962), Expect = e-108 Identities = 189/442 (42%), Positives = 273/442 (61%), Gaps = 3/442 (0%) Query: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 L+R L RHI+ +A+G AIGTGLF GS I +AGP+++ Y+I G +F VMRA+GE+ Sbjct: 18 LRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 77 Query: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 + N SF +A+ LGP AG+ GWTY F V+ G+ADV A Y WFP S W+ Sbjct: 78 LSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQLWFPGFSIWMS 137 Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187 L + LN+ VK+FGEMEFW +++K+ AIVA+I+ G ++ + G +S Sbjct: 138 ALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGIVLVSMHYPSPNGTTASLS 197 Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 N+W GG P G+ G A F + +FAF GIE++G A E KDP VLPRAINA+P+RI++ Sbjct: 198 NIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLPRAINAIPVRIIM 257 Query: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307 FYVL +LV+M++ PW Q+ SPFV++F +G+ +AA+I+N VV+T+A S+ NS IF Sbjct: 258 FYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVNFVVLTSAASSANSGIFST 317 Query: 308 GRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPE--NVFLLIASI 365 RM+FGLA+ G A K F LS VP + + LL+GV L YLIP+ VF ++ ++ Sbjct: 318 SRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVALIYLIPDVMTVFTMVTTV 377 Query: 366 ATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFP 425 + ++VW +IL + +A R+ A KF +P + +AF FV +L Sbjct: 378 SAILFMFVWTIILCSYLAYRKQHPQRHAAS-KFKMPLGKFMCWVCMAFFAFVLVLLTLQE 436 Query: 426 DTQAALIVGVVWIVLLVLAYLM 447 DT+ AL+V +W V+L L +L+ Sbjct: 437 DTRQALMVTPLWFVILTLGWLL 458 Lambda K H 0.329 0.142 0.441 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: 650 Number of extensions: 36 Number of successful extensions: 2 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: 468 Length of database: 463 Length adjustment: 33 Effective length of query: 435 Effective length of database: 430 Effective search space: 187050 Effective search space used: 187050 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 (21.8 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