Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate AZOBR_RS24095 AZOBR_RS24095 ABC transporter
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__azobra:AZOBR_RS24095 Length = 367 Score = 236 bits (601), Expect = 1e-66 Identities = 135/301 (44%), Positives = 184/301 (61%), Gaps = 9/301 (2%) Query: 23 LKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDIMLDGVRINDIPTNKRDVH 82 L+ E+ G+F TLLG SGSGK+T+L +I GL++ + G I++DG P +KRD+ Sbjct: 38 LEPTRLEVPAGEFLTLLGPSGSGKTTLLQMICGLVEPSGGRILIDGQDETRTPVHKRDIG 97 Query: 83 TVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAEVLKMVQLEGYEKRSIRKLSGGQ 142 VFQ YALFPH+ V EN+ FPLR+R + ++ +RV E L+MV L R ++LSGGQ Sbjct: 98 LVFQHYALFPHLTVAENIGFPLRMRGVAPADLTRRVKEALEMVHLGHLAGRFPKELSGGQ 157 Query: 143 RQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELRELQQRLGITFVFVTHDQEEAL 202 +QRVA+AR + QP V+L+DEPL ALD KLR MQYE++ L + G T ++VTHDQEEAL Sbjct: 158 QQRVALARCFVYQPSVILMDEPLGALDKKLREHMQYEIKRLHRETGATIIYVTHDQEEAL 217 Query: 203 AMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGESNILPGTMIED-----YLVEFN 257 AMSD I +MN I Q GTP DIY P F A FIG SNI G + D LV N Sbjct: 218 AMSDRICLMNHARIEQLGTPHDIYARPKTAFAADFIGVSNIFRGQVRRDGSGAPMLVTGN 277 Query: 258 GKRFEAVDGGMKPNEPVEVVIRPEDLRITLPEEGKLQVKVDTQLFRGVHYEIIAYDELGN 317 G + D +P+ +V+RPE L I + +++ +V ++ G ++ LG Sbjct: 278 GSFRLSADTPDRPDG--ALVVRPEQLDIDGDGDNEVRGEVVDTVYAGSETRVLV--SLGG 333 Query: 318 E 318 E Sbjct: 334 E 334 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: 326 Number of extensions: 15 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: 367 Length adjustment: 30 Effective length of query: 355 Effective length of database: 337 Effective search space: 119635 Effective search space used: 119635 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: 50 (23.9 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