Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate GFF1371 PGA1_c13880 putative transporter, BCCT family
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__Phaeo:GFF1371 Length = 545 Score = 770 bits (1988), Expect = 0.0 Identities = 371/539 (68%), Positives = 439/539 (81%), Gaps = 1/539 (0%) Query: 6 NGGIKRPDGKVNAIDTDYQIGQDNVALKVGPFGLDIHNRVFAISGMAIVLFVVATLTFRQ 65 N GI PDG+ IDT+Y+IGQDN+ VGP G DIHN VF +SG++I+LFV L + Sbjct: 7 NQGIPAPDGEAAVIDTEYEIGQDNLEGSVGPIGFDIHNPVFMVSGISIMLFVFYALVLPE 66 Query: 66 QVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTPLGRVRIGGTEATPDYSYAGWL 125 Q FF LR + S+ DWFFL++GN FV+ C LIV+P G+VR+GG +A PDY+Y GW Sbjct: 67 QAAAFFGWLRPAVTSSFDWFFLSAGNFFVLFCFFLIVSPWGKVRLGGADAAPDYTYTGWF 126 Query: 126 AMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNI-ENGVRTDWAPLGGAVGDTDAASALGM 184 AMLFAAGMGIGL+F+GVSEPMSH+S++ GGV++ ENG RTDWAPLGGA GD+ + LGM Sbjct: 127 AMLFAAGMGIGLMFYGVSEPMSHYSTSFGGVSMGENGARTDWAPLGGAAGDSAESVRLGM 186 Query: 185 AATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFYPLFGERVWGWVGHIIDILAV 244 AATIYHW LHPW+IYA++AL LA+FSFNKGLPLT+RS FYP+FGERVWGW GHIIDILAV Sbjct: 187 AATIYHWGLHPWAIYAIVALSLALFSFNKGLPLTIRSAFYPIFGERVWGWTGHIIDILAV 246 Query: 245 VATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVLIVVITALALISVVAGLDSGVKR 304 AT+FGLATSLG+GA+QA GLN LFGVP+ TT+VVLI ITA+ALISV+ GLD GVK Sbjct: 247 FATLFGLATSLGFGATQANAGLNELFGVPVGATTEVVLISAITAVALISVLRGLDGGVKI 306 Query: 305 LSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITNIPALSMPFEREDVNYSQGWTA 364 LSEINM LA +LL FV++VGPT+ I+TGFFD++ +Y+ +PALSMPF RED NYSQGWTA Sbjct: 307 LSEINMGLAFLLLIFVLLVGPTLLIITGFFDSLLAYVQYLPALSMPFGREDANYSQGWTA 366 Query: 365 FYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIPSTVCVLWMTAFGGTAISQYVNDG 424 FYWAWWISWSPFVGMFIARVSRGR+VREFIICV+LIPS VCVLWM+ FGGTAI Q V DG Sbjct: 367 FYWAWWISWSPFVGMFIARVSRGRTVREFIICVLLIPSLVCVLWMSVFGGTAIHQVVADG 426 Query: 425 YEAVFNAELPLKLFAMLDVMPFAEITSVVGIILVVVFFITSSDSGSLVIDTIAAGGKVDA 484 Y + L LKLF MLD +P A ITS VGI+LV+VFF+TSSDSGSLVIDTI AGGKVDA Sbjct: 427 YTGAQDTALELKLFKMLDQLPLAAITSFVGILLVIVFFVTSSDSGSLVIDTITAGGKVDA 486 Query: 485 PTPQRVFWCTFEGLVAIALMLGGGLAAAQAMAVTTGLPFTIVLLVATVSLIKGLMDEPR 543 P PQRVFWC FEG VAI L+LGGGL A QAM ++TGLPFT+VLL+ ++++GL E R Sbjct: 487 PMPQRVFWCVFEGAVAIVLLLGGGLVALQAMVISTGLPFTVVLLLMCWAIVRGLQTETR 545 Lambda K H 0.327 0.141 0.435 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: 1019 Number of extensions: 50 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: 553 Length of database: 545 Length adjustment: 36 Effective length of query: 517 Effective length of database: 509 Effective search space: 263153 Effective search space used: 263153 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: 53 (25.0 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