Align Large component of TRAP-type D-gluconate transporter (characterized)
to candidate CCNA_01515 CCNA_01515 C4-dicarboxylate transporter large subunit
Query= reanno::azobra:AZOBR_RS15920 (426 letters) >FitnessBrowser__Caulo:CCNA_01515 Length = 426 Score = 298 bits (764), Expect = 2e-85 Identities = 161/423 (38%), Positives = 249/423 (58%), Gaps = 13/423 (3%) Query: 1 MALAVFLSSLFGLMLLGMPIAFALMLTGVALMVHLDFFDAQLVA-QNMLSGADNYPLMAV 59 M L + L L L+++G+P+AFAL L + + +D A +VA Q + +G + + LMA+ Sbjct: 1 MELTLLLGLLALLLIIGVPVAFALGLASLVTFIFMDI--APVVAFQRIATGVNVFSLMAI 58 Query: 60 PFFILAGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALA 119 PFFI AG+LM GI++R++ +A + +G IRGGLG V +GAS+M +SGSA+A +AL Sbjct: 59 PFFIFAGDLMQQAGIAERLVRVADAAMGRIRGGLGVVDVGASMMFGGVSGSAVASVSALG 118 Query: 120 TLLIPMMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIFGVTTNTSIS--GLFMAGIVP 177 + LIP+M++ GY + + ++ I+ +IPPS II+ S+S LF+AG++P Sbjct: 119 STLIPLMKEKGYDADYAVNVTSTSAILGILIPPSHNMIIYAAAAGVSVSVADLFLAGVLP 178 Query: 178 GLLMGAGLVIT-WMFVVRGMTVKLQPKAS---WGERRTALVEGVWALALPVIIIGGLRGG 233 G+L G L W+ VR + PK W A + L VII GG+ GG Sbjct: 179 GILTGIFLAAAAWIIAVR----RGYPKGEFPGWPAFAAAFASALPGLLTAVIIFGGVLGG 234 Query: 234 IFTPTEAAVVAAVYSLVVALFVYRQVTLKDLVPLLVQAARTTSTVMFLCAAALVSSYMVT 293 +FTPTE++ VA +Y+LV+A+ VYR + + A +TT+ VM + +A +++ Sbjct: 235 VFTPTESSAVAVIYTLVIAVIVYRTLGFRGFTTAAQNAVKTTAMVMLIIGSAAAFGWLLA 294 Query: 294 LADLPQQMNEMLAPLLHEPKLLMVAITLLLLAVGTVMDLTPTILVLGPVLTPLAAAAGID 353 L + P+Q+ +L L P L+++ I L+LL +GT MD+ P I++ P+ P+A A G+D Sbjct: 295 LLEAPEQLATLLQTLTDNPILILLLINLILLILGTFMDMAPLIVITSPIFLPVAMATGMD 354 Query: 354 PTYFGVMFVLTGTLGLIHPPVCTVLNVVCGVARISLESATRGIWPFLLTYLLLLCLLIAV 413 P FG+M +L +GL+ PPV +VL V C V +I +E A R IWPF L L + V Sbjct: 355 PVQFGIMMMLNLGIGLVTPPVGSVLFVGCAVGKIKVEQAVRTIWPFYLALFAALMAITFV 414 Query: 414 PEI 416 P + Sbjct: 415 PAL 417 Lambda K H 0.328 0.142 0.420 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: 418 Number of extensions: 17 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: 426 Length of database: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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: 51 (24.3 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