Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate WP_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter
Query= uniprot:Q4KIP0 (466 letters) >NCBI__GCF_002095475.1:WP_084934657.1 Length = 463 Score = 351 bits (901), Expect = e-101 Identities = 184/455 (40%), Positives = 272/455 (59%), Gaps = 14/455 (3%) Query: 9 ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEM 68 +L+R L NRHIQLIA+GGAIGTGLF+GS + AGPS+I Y I GF+ F +MR +GE+ Sbjct: 17 KLRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGEL 76 Query: 69 IVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWPEIPTWV 128 ++ SFS FA G + G+ GW YW +V+ G+A++ A+ Y Q W+P W+ Sbjct: 77 LLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQLWFPGFSIWM 136 Query: 129 SAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYML---FSGSGGSQASV 185 SA + +N+ VK FGE EFWFAIIK+VAIV +I+ G ++ + G+ AS+ Sbjct: 137 SALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGIVLVSMHYPSPNGTTASL 196 Query: 186 SNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVYRVL 245 SN+W HGG FP G +G +F+F G+ELVG AAE +P KV+P+AIN + R++ Sbjct: 197 SNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLPRAINAIPVRII 256 Query: 246 IFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLTAAL 305 +FYV AL V++++ PW+++L + SPFV++F LIG AAA I+NFVVLT+A Sbjct: 257 MFYVLALLVIMAVTPWNQVLP---------NRSPFVEMFVLIGLPAAASIVNFVVLTSAA 307 Query: 306 SVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLAPHE 365 S NSG++ SRML+GLAE G A KA +L+ + VP L S L L+ V + YL P Sbjct: 308 SSANSGIFSTSRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVALIYLIPDV 367 Query: 366 ALELLFALVVAAL--MINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAFMVM 423 V+A+ M W +I ++L +RK ++ FK ++C+AF Sbjct: 368 MTVFTMVTTVSAILFMFVWTIILCSYLAYRKQHPQRHAASKFKMPLGKFMCWVCMAFFAF 427 Query: 424 IVGVMWMIPGIRASVYAIPVWVLVIWGFYLLSRAK 458 ++ ++ + R ++ P+W +++ +LL R K Sbjct: 428 VLVLLTLQEDTRQALMVTPLWFVILTLGWLLRRRK 462 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: 686 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: 463 Length adjustment: 33 Effective length of query: 433 Effective length of database: 430 Effective search space: 186190 Effective search space used: 186190 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