Align Transporter, component of The methionine/alanine uptake porter, MetPS (Trotschel et al., 2008) (MetP is the transporter; MetS is an essential auxiliary subunit) (characterized)
to candidate 353168 BT3642 Na+-dependent transporter (NCBI ptt file)
Query= TCDB::Q8NRL8 (579 letters) >FitnessBrowser__Btheta:353168 Length = 456 Score = 209 bits (532), Expect = 2e-58 Identities = 146/419 (34%), Positives = 215/419 (51%), Gaps = 31/419 (7%) Query: 34 REVFSSRSVFILAAIGSAVGLGNIWRFPYVAYDNGGGAFLIPYAIALLTAGIPLLFLDFA 93 R F S+ ILA+ GSAVGLGNIWRFPY ++GG AF++ Y + G+P+L +F Sbjct: 6 RANFGSKLGVILASAGSAVGLGNIWRFPYETGNHGGAAFILIYLGCVFLLGLPILIAEFL 65 Query: 94 IGHRYRGSAPLAFRRFKKQT--ETIGWIQVGIAFFITIYYAAIIGWAGLYAFKSLNKAWG 151 IG R R + A+++ T +G + V AF I YY+ + GW Y +++L + Sbjct: 66 IGRRSRANTAGAYQKLAPGTHWRWVGRMGVLAAFLILSYYSVVAGWTLEYVYEALTNGFT 125 Query: 152 ADPDTYFFSDFLNFDSEAVVSMDIVPQIAIALFIVWIAAIVVLAIGVDKGIGRVSMVFMP 211 T F S F F S P + + LF++ I+V GV+KGI + S + MP Sbjct: 126 GKTPTEFISSFQQFSSS-----PWRPVLWLVLFLLVTHFIIVK--GVEKGIEKSSKIMMP 178 Query: 212 LLVIIFLIVVIQAVLLPGAEIGLDALFTPNWEALKNPTVWIAAYGQIFFSLSVGFGIMLT 271 L II LI+VI +V LPGA G++ L P++ + + V+++A GQ FFSLS+G G + T Sbjct: 179 TLFIIILILVICSVTLPGAGAGIEFLLKPDFSKV-DGNVFLSAMGQAFFSLSLGMGCLCT 237 Query: 272 YSSYLKPRTNLTSTGLVTGFANSSFEVLAGIGVFAALGFMAANAGVGVDEVATSGIGLAF 331 Y+SY TNLT T G ++ VLAG +F A A + G+ D +G L F Sbjct: 238 YASYFSKETNLTKTAFSVGIIDTFVAVLAGFIIFPA----AFSVGIQPD----AGPSLIF 289 Query: 332 VAFPAIINE----MP-LGGLFGFLFFSSLTIAGFTSLFSLLEVVVSAVKDKFGLNR-KAT 385 + P + + +P L +F +F+ L +A TS SL EVV + + ++F R KA Sbjct: 290 ITLPNVFQQAFSGVPILAYIFSVMFYVLLAMAALTSTISLHEVVTAYLHEEFNFTRGKAA 349 Query: 386 AIGVG-----VVMALLSLGLFS--TTSGLATLDIMDKFTNNIGIVAVALIAVVSIDWVL 437 + G ++ LSLG+ T GL D+ D T I + L + W L Sbjct: 350 RLVTGGCIFLGILCSLSLGVMKGFTIFGLGIFDLFDFVTAKIMLTLGGLCISIFTGWYL 408 Lambda K H 0.325 0.141 0.430 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: 622 Number of extensions: 23 Number of successful extensions: 3 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: 579 Length of database: 456 Length adjustment: 35 Effective length of query: 544 Effective length of database: 421 Effective search space: 229024 Effective search space used: 229024 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: 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