Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate AO353_16120 AO353_16120 D-alanine/D-serine/glycine permease
Query= uniprot:Q4KIP0 (466 letters) >FitnessBrowser__pseudo3_N2E3:AO353_16120 Length = 472 Score = 399 bits (1024), Expect = e-115 Identities = 208/465 (44%), Positives = 292/465 (62%), Gaps = 15/465 (3%) Query: 3 QTLKQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIM 62 +T + G LKR L RHI+L+ALG IG GLFLGSA ++ AGP+++L Y I G +IM Sbjct: 11 ETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIM 70 Query: 63 RQLGEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWP 122 R LGEM V PVAGSFS +A Y G GFL GWNYW L+++ +AE+TAV Y+ W+P Sbjct: 71 RALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFP 130 Query: 123 EIPTWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYMLFSGSG--G 180 E+P W+ A V + IN++ VK FGE EFWFA+IK+V I+ M+V G ++ G G G Sbjct: 131 EVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVVGGVGVIAFGFGNDG 190 Query: 181 SQASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQV 240 +SNLWSHGGF PNG G+LM++ +MF++ G+E++G+TA EA P+K IP AI V Sbjct: 191 VALGISNLWSHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSV 250 Query: 241 VYRVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVV 300 +R+L+FYVGAL V+LS+YPW+E+ SPFV F +G AA I+NFVV Sbjct: 251 FWRILLFYVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFVV 301 Query: 301 LTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNY 360 +TAALS N G++ RMLY LA+ G AP K GVP AL +S LL VL+NY Sbjct: 302 ITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAK-TSNGVPRRALLLSIGALLLGVLLNY 360 Query: 361 LAPHEALELLFALVVAALMINWALISLTHLRFRKAM--AEQGVVPSFKAFWSPLSNYLCL 418 L P + + A+ + W +I L L+FRK + AE+ + ++ + P+S+YL L Sbjct: 361 LVPEKVFVWVTAIATFGAIWTWVMILLAQLKFRKGLSPAERAAL-KYRMWLYPVSSYLAL 419 Query: 419 AFMVMIVGVMWMIPGIRASVYAIPVWVLVIWGFYLLSRAKKASQP 463 AF+VM+VG+M P R ++Y P +++++ + + + + P Sbjct: 420 AFLVMVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTGVP 464 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: 750 Number of extensions: 46 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: 472 Length adjustment: 33 Effective length of query: 433 Effective length of database: 439 Effective search space: 190087 Effective search space used: 190087 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 17 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