Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= TCDB::M1IW84 (556 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 327 bits (839), Expect = 5e-94 Identities = 182/454 (40%), Positives = 268/454 (59%), Gaps = 17/454 (3%) Query: 17 LRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIGFFVFFVLRAMGELL 76 L+R L NRHIQLIA+GGAIGTGLF+GS + AGP++++ Y I GF F ++R +GE++ Sbjct: 11 LQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIMRQLGEMI 70 Query: 77 LSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPIWVP 136 + SF FA G AGF GW+YW +V+ G+A+L A+ Y +FWWP +P W Sbjct: 71 VEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWAT 130 Query: 137 ALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHATIE 196 A LI +NL +V+ FGE EFWFA++KVAAIV +I +G L+ + G A+I Sbjct: 131 AAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVS---GKGGEQASIS 187 Query: 197 NLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLRVAV 256 NLW+ GFFP GF G++ I F++ G+ELVG AAE A+P+ +P+AIN V R+ + Sbjct: 188 NLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRILI 247 Query: 257 FYIGALLAILAVVPWRQF-----ASGE----SPFVTMFSLAGLAAAASVVNFVVVTAAAS 307 FYIGAL +LA+ PW A+G+ SPFV +FSL G AA ++NFVV+TAA S Sbjct: 248 FYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAALS 307 Query: 308 SANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRSVI 367 NSG + RML+GLA++G AP + ++N GVP A+ ++A + L + + Y Sbjct: 308 VYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQ-- 365 Query: 368 GAFTLVTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTDSVYKMPGGVVMCWAVLVFFAFV 427 GA L+ +++ + WAMI +++L +RR Q+ + +K + + L F A + Sbjct: 366 GALELLMSLAVAALVINWAMISLAHLKFRRAMQQQGVEPSFKAFWFPLSNYLCLAFVAGI 425 Query: 428 IWTLTTETETATALAWFPLWFVLLAVGWLVTQRR 461 + + ++ P+W L WL + R Sbjct: 426 LIIMLWLPGIRMSVFAIPVWVGFL---WLCYRLR 456 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: 694 Number of extensions: 34 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: 464 Length adjustment: 34 Effective length of query: 522 Effective length of database: 430 Effective search space: 224460 Effective search space used: 224460 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