Align Ectoine/glycine betaine/proline transporter EctP (characterized)
to candidate WP_067477459.1 BJL86_RS14655 BCCT family transporter
Query= SwissProt::Q79VE0 (615 letters) >NCBI__GCF_001659785.1:WP_067477459.1 Length = 632 Score = 303 bits (775), Expect = 2e-86 Identities = 180/541 (33%), Positives = 289/541 (53%), Gaps = 25/541 (4%) Query: 25 IFSISVGFIVVFVIATIALGEKARTTFSAIAGWLLENLGWMYIGGVSLVFIFLMGIFA-S 83 +F+ + IV F+ I + T S + GW +ENLGW+ + V ++ + +M A S Sbjct: 43 LFATTAALIVAFIAWGIIDPDSVGTVSSTMFGWAIENLGWL-LNIVMILGLAVMTYLAFS 101 Query: 84 RYGRVKLGDDDDDPEHTLIVWFCMLFAGGVGAVLMFWGVAEPINHAFNVPMANEESMSEA 143 R+GR+KLG DD++PE L W M+F G+G + F+G +EP++H P + + + Sbjct: 102 RFGRIKLGKDDEEPEFALFSWVAMMFGAGIGVGIFFFGPSEPLSHYLTPPPHSVDPETPE 161 Query: 144 AIVQAFAYTFYHFGIHMWVIMALPGLSLGYFIYKRKLPPRLSSVFSPILGK-HIYSTPGK 202 A+ + A + +H+G+ +W + A+ G +L Y Y+R LSSVF ++G G Sbjct: 162 ALHLSMAQSHFHWGLMIWALYAMVGGALAYSSYRRGRVTLLSSVFKSLIGSDRSEGLAGS 221 Query: 203 LIDVLAIVGTTFGIAVSVGLGVLQINAGMNKLWSTPQVSWVQLLIIL-IITAVACISVAS 261 +ID++AI+ T FG A ++GL +QI G+ + +V+ L++I+ I+TA +S S Sbjct: 222 IIDMMAIIATLFGTAATLGLSAIQIGQGVQIVSGVSEVTNTVLIVIIGILTACFIVSAVS 281 Query: 262 GLDKGIKLLSNINIAMAVALMFFILFTGPTLTLLRFLVESFGIYASWMPNLMFWTDSF-Q 320 G+ +GI+ LSN+NI + + L+ F+ GPTL LL + YA + ++M S+ Q Sbjct: 282 GVSRGIRYLSNLNITLTLGLILFVFLLGPTLFLLNLVPAGILSYADNLLDMMSRGLSWGQ 341 Query: 321 DNPGWQGKWTVFYWAWTICWSPYVGMFVARISRGRTVREFIGGVLALPAIFGVVWFSIFG 380 D +Q WT FYWAW I W+P+VGMF+ARISRGRT+R+F P ++ F+IFG Sbjct: 342 DTIEFQAVWTSFYWAWWIAWTPFVGMFIARISRGRTIRQFALVTTLAPTFILILAFTIFG 401 Query: 381 RAGIEVELSN-PGFLTQPTVVEGDVPA--ALFNVLQEYPLTGIVSAFALVIIVIFFITSI 437 I + PGF +G + LF++ PL + + ++ +FFITS Sbjct: 402 GTAISFSREDFPGF-------DGSASSENVLFSLFDNLPLGTVTPLIIIFVLAVFFITSA 454 Query: 438 DSAALVNDMFATGAENQTPTSYR---VMWACTIGAVAGSLLIISPSSGIATLQEVVIIVA 494 DSA++V T +E P + V W + +A +L++ + + LQ + I++A Sbjct: 455 DSASVV---MGTLSEKGNPAPNKLIVVFWGLCMMGIAVVMLLVGGETALTGLQNLTILIA 511 Query: 495 FPFFLVQFVMMFSLLKGMSEDAAAVRRVQTRQWEKTDTPEKLEEHSS----QPAPGYDDE 550 PF +V + + LK +S D AA+RR + K + LEEH AP D Sbjct: 512 IPFSVVLVGLAVAFLKDLSTDPAAIRRTYAQTAIKNAVVKGLEEHGDDFEISVAPSTDGR 571 Query: 551 G 551 G Sbjct: 572 G 572 Lambda K H 0.324 0.140 0.434 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: 1058 Number of extensions: 50 Number of successful extensions: 7 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: 615 Length of database: 632 Length adjustment: 37 Effective length of query: 578 Effective length of database: 595 Effective search space: 343910 Effective search space used: 343910 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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