Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate WP_015448129.1 R2APBS1_RS12170 D-serine/D-alanine/glycine transporter
Query= uniprot:Q4KIP0 (466 letters) >NCBI__GCF_000230695.2:WP_015448129.1 Length = 465 Score = 347 bits (890), Expect = e-100 Identities = 184/449 (40%), Positives = 269/449 (59%), Gaps = 14/449 (3%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 69 L+R L NRH+QLIA+GGAIGTGLF+GS + AGPS++L Y I G + F +MR +GE++ Sbjct: 11 LRRSLSNRHLQLIAIGGAIGTGLFMGSGKTISLAGPSILLVYLIIGVMLFFVMRAMGELL 70 Query: 70 VEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWPEIPTWVS 129 + SF F+ G + GF GW YW +V+ +A++ A+ Y QFW+P + W+ Sbjct: 71 LSNLEYKSFIDFSTDLLGPWAGFFCGWTYWFCWVITAIADVIAIAAYAQFWFPGLAPWIP 130 Query: 130 AAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYML---FSGSGGSQASVS 186 A + +L+ +N++ VK FGE EFWFA+IK+VAIV +I G ++ F+ G +AS++ Sbjct: 131 AVLCVLLLLSLNLVTVKLFGELEFWFALIKIVAIVALIATGFALVAWGFTSPSGHKASLA 190 Query: 187 NLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVYRVLI 246 NLWS GGFFP G +G +F+F G+ELVG TAAE A+P++ +PKAIN + R++I Sbjct: 191 NLWSDGGFFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETADPKRNLPKAINSIPVRIII 250 Query: 247 FYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLTAALS 306 FYV AL ++ + PW + AG SPFV++F L G AAA ++NFVVLT+A S Sbjct: 251 FYVLALIAIMVVTPWR----LVEAG-----KSPFVELFVLAGIPAAASLINFVVLTSATS 301 Query: 307 VYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLAPH-- 364 NSG++ SRMLYGLAE+ APK +L++ VP L L S LL + YL P Sbjct: 302 SANSGIFSTSRMLYGLAEEQHAPKTFARLSRAAVPSLGLLFSCFCLLLGAAMIYLIPDLI 361 Query: 365 EALELLFALVVAALMINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAFMVMI 424 A L+ L M W+LI ++ +R+ + +K + CLAF V + Sbjct: 362 TAFTLITTLSAVLFMFVWSLILFGYIAYRRQRPQLHQASIYKMPGGVFMCWACLAFFVFV 421 Query: 425 VGVMWMIPGIRASVYAIPVWVLVIWGFYL 453 + ++ + P R ++ A PVW +++ YL Sbjct: 422 LVLLSLQPDTREALIASPVWFVLLGIGYL 450 Lambda K H 0.327 0.141 0.440 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: 697 Number of extensions: 40 Number of successful extensions: 5 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: 466 Length of database: 465 Length adjustment: 33 Effective length of query: 433 Effective length of database: 432 Effective search space: 187056 Effective search space used: 187056 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