Align The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized)
to candidate Pf6N2E2_883 Major myo-inositol transporter IolT
Query= TCDB::A2R3H2 (518 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_883 Length = 472 Score = 186 bits (473), Expect = 1e-51 Identities = 139/467 (29%), Positives = 222/467 (47%), Gaps = 34/467 (7%) Query: 12 LTAVAYSGSLLFGYDTGVMGSVLSLTSFKEDFGIPTGSSGFASSKSSEISSNVVSLLTAG 71 +T +A G LLFG+DTGV+ +L K+D G+ + G V S L G Sbjct: 31 ITWIATFGGLLFGFDTGVING--ALLYMKDDLGLTPFTEGL-----------VASALLIG 77 Query: 72 CFFGAIFAAPLNERIGRRYALMIFTVIFLIGAAVQVASKHHIGQIYGGRVIAGLGIGGMS 131 GA+F+ L++ GRR ++ V+F +GA + A + + R GL +GG S Sbjct: 78 AMMGALFSGRLSDLKGRRRIILFLAVVFFLGA-LACALAPTLDVMVAARFTLGLAVGGAS 136 Query: 132 SITPVFVSENCPPSIRGRVAGMFQEFLVIGSTFAYWLDYGVSLHIPSSTKQWRVPVAVQL 191 + P ++SE P SIRGR+ + +V G A+ + + WR +A+ Sbjct: 137 VVVPAYLSEMAPSSIRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALAT 196 Query: 192 IPGGLMLLGLFFLKESPRWLAGKGRHEEALQSLAYIRNESPDSEEIQKEFAEIRAAIDEE 251 +P + LG+ ++ ESPRWLA KGR E L+ L +R E E++ I I E Sbjct: 197 LPAVALWLGMLYMPESPRWLATKGRFREGLEVLKLVREEYYAKAEME----AITQQISNE 252 Query: 252 VAATEGLTYKEFIQPSNLKRFGFAFTLMLSQQFTGTNSIGYYAPEIFQTIGLSATNSSLF 311 +G +++ Q + F + ++ Q TG NSI Y+ +I GL S+L Sbjct: 253 RFIKKG-GWRDLSQKGARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLE-QRSALI 310 Query: 312 ATGVYGTVKVVATAIFLFVGI---DRWGRKLSLVGGSIWMASMMFIIGAVLATHPPDTSA 368 A V G + + AT FVGI DR GR+ ++ G + +IG V P + Sbjct: 311 ANVVNGIISIGAT----FVGIALLDRVGRRPMMLLGFTGTTLSLLLIGLVSVFVDPSVTR 366 Query: 369 SGVSQASIAMVVMIYLYVIGYSASWGPTPWVYVSEIFPTRLRSYGVGLAATSQWLWSFVV 428 + + ++AM ++ GP WV ++EIFP R+R +G+A + WL + ++ Sbjct: 367 AMLILGAMAM------FLASMQGLIGPAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMI 420 Query: 429 TEITPKAVHNIG-WRTFLMFGIFCVAMCVFVIVFAKETKGRSLEDMD 474 P V IG +TF +F + FV V+ ET+G +LE+++ Sbjct: 421 GMFFPSLVAMIGIGQTFFVFVGAGLLSLTFVAVWVPETRGSTLEEIE 467 Lambda K H 0.323 0.137 0.411 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: 581 Number of extensions: 34 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: 518 Length of database: 472 Length adjustment: 34 Effective length of query: 484 Effective length of database: 438 Effective search space: 211992 Effective search space used: 211992 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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