Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= uniprot:A0A0C4YP23 (465 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 675 bits (1741), Expect = 0.0 Identities = 329/446 (73%), Positives = 388/446 (86%) Query: 8 NTDATLKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQ 67 +T L+RGLKNRHIQLIALGGAIGTGLFLGIAQTI++AGPSVLLGYA+AG++AF IMRQ Sbjct: 5 STPERLQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFLIMRQ 64 Query: 68 LGEMVVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHI 127 LGEMVV+EPVAGSFSHFA++Y FAGF+SGWNYWV+Y+LV MAEL+AVGIYVQYWWP Sbjct: 65 LGEMVVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDF 124 Query: 128 PTWASALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTAGPQAS 187 PTWA+A FF++IN INLT VK +GEMEFWF++VKV+AIV MI FG +LL SG GP AS Sbjct: 125 PTWATAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGAWLLGSGHGGPDAS 184 Query: 188 VSNLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRI 247 V+NLWQ+GGFFPNG++GLVMA+AVIMFSFGGLELVGITAAEAD P ++IPKATNQV+YRI Sbjct: 185 VANLWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVVYRI 244 Query: 248 LIFYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGVY 307 LIFY+GAL VLLSLYPW+KVV GGSPFV+IFH ++SD+VAT+LN VVLTAALSVYNS VY Sbjct: 245 LIFYIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYNSCVY 304 Query: 308 CNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMGL 367 NSRMLFGLA QG+AP+ LLKV++ G+PL AL VSA AT CV+INY MPG AF LLM L Sbjct: 305 ANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAFGLLMAL 364 Query: 368 VVSALIINWAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMYLTPG 427 VSAL+INWA ISI HLKFR+ K AAG +KSLG+PLTNY+CLAF+ IL VMYLTP Sbjct: 365 AVSALVINWASISITHLKFRKAKLAAGITPFYKSLGHPLTNYLCLAFIVLILVVMYLTPP 424 Query: 428 LRISVYLIPAWLAVLGLSYRLRQKQK 453 +RISV LIPAW+AVL ++++L++ ++ Sbjct: 425 IRISVMLIPAWIAVLWVAFKLKKARQ 450 Lambda K H 0.326 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: 688 Number of extensions: 27 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: 465 Length of database: 453 Length adjustment: 33 Effective length of query: 432 Effective length of database: 420 Effective search space: 181440 Effective search space used: 181440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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