Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate PP_4495 PP_4495 aromatic amino acid transport protein
Query= TCDB::M1IW84 (556 letters) >FitnessBrowser__Putida:PP_4495 Length = 472 Score = 328 bits (841), Expect = 3e-94 Identities = 172/455 (37%), Positives = 264/455 (58%), Gaps = 14/455 (3%) Query: 17 LRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIGFFVFFVLRAMGELL 76 L+R L NRHIQLIA+GGAIGTGLF+GS + AGP++++ Y I GF F ++R +GE++ Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVMKSAGPSMILGYAICGFIAFMIMRQLGEMI 70 Query: 77 LSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPIWVP 136 + SF FA G AGF GW+ W +++ G+++L A+ Y +WWP +P WV Sbjct: 71 VEEPVAGSFSHFAHTYWGGFAGFLSGWNCWVLYILVGMSELSAVGKYVHYWWPEIPTWVT 130 Query: 137 ALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHATIE 196 A LI A+NL +V+ FGE EFWFA+IKV AIV +I +GA L+ + P AT+ Sbjct: 131 AAAFFVLINAINLMNVKFFGEAEFWFAIIKVVAIVSMIGLGAYLLTSGSGGP---EATVA 187 Query: 197 NLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLRVAV 256 NLW GFFP G G+V F++ G+E++G AAE P+ +P+AIN V R+ + Sbjct: 188 NLWTHGGFFPNGVSGLVMALAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILI 247 Query: 257 FYIGALLAILAVVPWRQFAS---------GESPFVTMFSLAGLAAAASVVNFVVVTAAAS 307 FY+GAL+ +L++ PW + G SPFV +FSL G AA+++NFVV+TAA S Sbjct: 248 FYVGALVVLLSLTPWDNLVASIDASGGSYGSSPFVQVFSLLGSDVAANLLNFVVLTAALS 307 Query: 308 SANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRSVI 367 NSG + RML G+A++G APA+ ++++ GVP ++L++A + ++ L Y Sbjct: 308 VYNSGTYCNARMLLGMAEQGDAPASLAKVDKRGVPVRSILVSAAVTFVAVLLNYLMPQ-- 365 Query: 368 GAFTLVTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTDSVYKMPGGVVMCWAVLVFFAFV 427 A L+ ++ + WAMI S+L +R+ + ++K + VL F + Sbjct: 366 NALELLMSLVVATLVINWAMISYSHLKFRQHLDRTGQKPLFKALWYPYGNYVVLAFVVLI 425 Query: 428 IWTLTTETETATALAWFPLWFVLLAVGWLVTQRRQ 462 + + ++ P+W + + V ++V RRQ Sbjct: 426 LGIMLMIPGIQVSVYAIPVWLLAMLVVYMVKSRRQ 460 Lambda K H 0.328 0.140 0.442 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: 609 Number of extensions: 27 Number of successful extensions: 4 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: 556 Length of database: 472 Length adjustment: 35 Effective length of query: 521 Effective length of database: 437 Effective search space: 227677 Effective search space used: 227677 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: 52 (24.6 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