Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= TCDB::M1IW84 (556 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 263 bits (672), Expect = 1e-74 Identities = 160/455 (35%), Positives = 243/455 (53%), Gaps = 12/455 (2%) Query: 17 LRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIGFFVFFVLRAMGELL 76 L++ L RHI +IA+GG IG GLF+GSG I+ AGPA ++ Y I G V V+ +GE+ Sbjct: 6 LKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPAAILSYLIGGVMVTLVMFMLGEMA 65 Query: 77 LSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPIWVP 136 N + SF +A LG AGF VGW YWF ++T + + + + + P LP+ Sbjct: 66 SRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWLPVPAG 125 Query: 137 ALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHAT-I 195 AL + ++A N +SVR FGE E+W + KVA I+ + +GA ++ F G+ A + Sbjct: 126 ALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASIL---FGLQPGIPAPGL 182 Query: 196 ENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLRVA 255 NL + GF P G V+SG + F+ G E+ AA E+ +P + + RAI +V LRV Sbjct: 183 LNLTDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILRVM 242 Query: 256 VFYIGALLAILAVVPWRQFASGESPFVTMFSLAGLAAAASVVNFVVVTAAASSANSGFFS 315 VFY+G++ ++ +PW A+ +SP+V++FS+AG AA + V+ + S NS FS Sbjct: 243 VFYVGSVSILILCMPWTDKANLKSPYVSLFSMAGFTGAAVAMKIVLFVSFMSVMNSFLFS 302 Query: 316 TGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRSVIGAFTLVTT 375 RMLF L+ GHAPA F + N GVP AL+L + ++ + + + + F ++ Sbjct: 303 NSRMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGGDL--FLMLAK 360 Query: 376 VSSLLFMFVWAMIIISYLVYRR--RHPQRHTDSVYKMPGGVVMCWAVLVFFAFVIWTLTT 433 S M VW II+++ RR +H QR S ++ V W L+ V+ + Sbjct: 361 SSGAFVMIVWIFIIVAHFAMRRQTKHEQRDPAS-FRAWFYPVSNWVALLALVAVLGSQAF 419 Query: 434 ETETATALAWFPLWFVLLAVGWLVTQRRQSRRSFG 468 E+ WF + L V W +RR SFG Sbjct: 420 NPESRFQF-WFAVSTALAIVAWYYVRRRHP--SFG 451 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: 612 Number of extensions: 37 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: 556 Length of database: 459 Length adjustment: 34 Effective length of query: 522 Effective length of database: 425 Effective search space: 221850 Effective search space used: 221850 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