Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 162 bits (409), Expect = 2e-44 Identities = 94/293 (32%), Positives = 154/293 (52%), Gaps = 7/293 (2%) Query: 39 GLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDA 98 G + D +L +++GE I+G SG GK+T++RL+ + G++ I G +I + Sbjct: 20 GDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRISGKEITQTPP- 78 Query: 99 ELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLENYA 158 ++ + VFQ +AL PH+ V DN AFG++L Q +K AL+ VG+ +Y Sbjct: 79 -----HKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVGMTDYE 133 Query: 159 HAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTI 218 + D LSGG +QRV +ARA+ P++LL+DE +ALD +R +MQ EL ++ T Sbjct: 134 YRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSLGITF 193 Query: 219 VFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKD 278 V+++HD +EA+ + D I +M G++ Q+GTP +I N P N +V F +I D Sbjct: 194 VYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGESNILNGTMIHD 253 Query: 279 -IARRSPVGLIRKTPGFGPRSALKLLQDEDREYGYVIERGNKFVGVVSIDSLK 330 + R GFG + + ++ + Y + + + GVV K Sbjct: 254 KLVRFCGTEFECVDEGFGENTPVDVVIRPEDLYIFPVSEMAQLTGVVQTSIFK 306 Score = 27.3 bits (59), Expect = 0.001 Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 5/65 (7%) Query: 300 LKLLQDEDREYGYVIERGNKFVGVVS-----IDSLKAALSQAQGIEAALIDDPLVVDAQT 354 LKL + + G ++ K VG+ +DSL Q I A++++P V+ Sbjct: 106 LKLKKTPKQTIGKKVKAALKMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDE 165 Query: 355 PLSEL 359 PL+ L Sbjct: 166 PLAAL 170 Lambda K H 0.319 0.137 0.378 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: 402 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 400 Length of database: 463 Length adjustment: 32 Effective length of query: 368 Effective length of database: 431 Effective search space: 158608 Effective search space used: 158608 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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