Align D-gluconate TRAP transporter, periplasmic component (characterized)
to candidate 8501405 DvMF_2135 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= reanno::psRCH2:GFF2082 (338 letters) >FitnessBrowser__Miya:8501405 Length = 365 Score = 158 bits (399), Expect = 2e-43 Identities = 99/313 (31%), Positives = 168/313 (53%), Gaps = 11/313 (3%) Query: 4 LLISTLAAALLGSTLSLGYAQAADDIRPRMIRFGYGLNEDSNQGRAAKLLAEEVAKASGG 63 L+++ LAA L G + A AA ++ ++ S Q A+ + + + S G Sbjct: 39 LMLACLAAILPGWPRT---ASAATELTLAVVT-----TPGSAQHVCAERFRQLLEERSHG 90 Query: 64 KLKVRTFASASLGSDDQMQNALIGGAQEMMVGSTATLVGISKEMAVWDTPFLFTDPRQAD 123 +V S +LG++ ++ L G ++ + + L E+ V D PFLF D +AD Sbjct: 91 AYRVVVHHSGTLGTETEILQQLQLGGVQLAIITLGVLDPFVPEVKVLDYPFLFRDAAEAD 150 Query: 124 QVLDGPVGRQVMDKLEEKGLVGLVYWENGFRNVTNSARPIEKLEDFNGVKLRVMPNPVFI 183 +VLDG GR ++D LE GL GL + ENGFR++TN+ RP+ ++D G+K+RV+ + + Sbjct: 151 RVLDGATGRALLDALERVGLKGLHFSENGFRHLTNNVRPVRSVDDVRGLKIRVLESTLHR 210 Query: 184 DTFKRMGANAVPLPFSELFTALETKAVDGQENPFNTILSSKFYEVQKYLSVTNHVYSPWI 243 + ++ +GAN P+ + ++ L+ +DGQENP + + EVQKYLS+T HVYS Sbjct: 211 ELWRALGANPTPMGW-PIYAELQQGTIDGQENPLWVMAEYRMPEVQKYLSLTGHVYSAHA 269 Query: 244 VTVSKRWWDGLSATEQGILMEAAEKARDAEREDTRREASQALAALKERGMQINEVSPDEI 303 + W++GL E+ ++M+ A +R R++ + L L+E GMQ+ V ++ Sbjct: 270 DLANLAWFNGLPPAERTLVMQCMADAAAYQRAYNRQKDADYLRRLREAGMQV--VDAPDL 327 Query: 304 QRMREKAQPAIQT 316 R +A Q+ Sbjct: 328 ASFRARADALRQS 340 Lambda K H 0.315 0.131 0.368 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: 230 Number of extensions: 7 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: 338 Length of database: 365 Length adjustment: 29 Effective length of query: 309 Effective length of database: 336 Effective search space: 103824 Effective search space used: 103824 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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