Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate AZOBR_RS26295 AZOBR_RS26295 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__azobra:AZOBR_RS26295 Length = 354 Score = 254 bits (650), Expect = 2e-72 Identities = 153/352 (43%), Positives = 216/352 (61%), Gaps = 24/352 (6%) Query: 6 IEFKNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDIM 65 IEF++V K + + K L D + + G+F T+LG+SGSGK+T LN +AG A +GDI Sbjct: 1 IEFQSVRKAY--GSVKALHDFSLTIRPGEFLTILGSSGSGKTTALNALAGFSTADSGDIR 58 Query: 66 LDGVRINDIPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAEVLKMV 125 +DG + D P +R++ VFQ+Y+LFPHM+VF+N+AFPLR+R++ +++I++RV VL++V Sbjct: 59 IDGRSVIDEPPERRNLGMVFQNYSLFPHMSVFDNIAFPLRMRRMPRRDIKERVERVLEIV 118 Query: 126 QLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELRELQQ 185 +L R R LSGGQ+QRVA ARAI+ +P V+L+DEPL ALDLKLR +Q+E++E+Q Sbjct: 119 RLGPLAGRMPRDLSGGQQQRVAFARAIVFEPPVLLMDEPLGALDLKLREALQFEIKEIQH 178 Query: 186 RLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGESNIL- 244 +LG T V+VTHDQ EALAMS I V+ DG I Q GTP ++YD P + FVA FIG++N+L Sbjct: 179 QLGCTVVYVTHDQREALAMSSRIVVLRDGRIEQVGTPSEMYDAPQSRFVADFIGQTNLLA 238 Query: 245 -----PGTM-IEDYLVEFNGKRFEAVDGGMKPNEPVEVVIRPEDLRITLPEEG---KLQV 295 PG++ I + V + F A G + IRPE L+ P EG + V Sbjct: 239 ADVAQPGSVAIPELGVTYRENAFTARPGSWYAS------IRPEKLQ-RRPAEGPDIAVSV 291 Query: 296 KVDTQLFRGVHYEIIAYDELG-----NEWMIHSTRKAIVGEEIGLDFEPEDI 342 + +F G E A + G E R GE L P D+ Sbjct: 292 TIQEAVFLGDVIEYSARTDHGALIHFREQRRDRDRIPERGETANLVLRPSDV 343 Lambda K H 0.318 0.138 0.386 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: 321 Number of extensions: 14 Number of successful extensions: 1 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: 385 Length of database: 354 Length adjustment: 30 Effective length of query: 355 Effective length of database: 324 Effective search space: 115020 Effective search space used: 115020 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 (21.7 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