Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate 3608728 Dshi_2120 ABC transporter related (RefSeq)
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__Dino:3608728 Length = 376 Score = 234 bits (596), Expect = 4e-66 Identities = 138/361 (38%), Positives = 212/361 (58%), Gaps = 22/361 (6%) Query: 3 KPIIEFKNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTG 62 +PI++F NV K F + +K +FE+ G+F ++G+SG GK+T L ++AGL D T G Sbjct: 12 EPIVKFDNVVKRF--GSFTAVKKADFEIGRGEFLAIMGSSGCGKTTTLRMLAGLEDPTEG 69 Query: 63 DIMLDGVRINDIPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAEVL 122 I LDG ++N T RD V+QS ALFP + V ENV F L++R I K+E QR + L Sbjct: 70 AIYLDGEQVNGKATWDRDTPMVWQSLALFPFLTVQENVEFALKMRGIGKEERRQRADKWL 129 Query: 123 KMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELRE 182 +Q+ + R+I +LSGGQ+QRVA+ARA++ +P+++LLDEPLSALD L+ MQ L Sbjct: 130 DKMQITEFADRNINQLSGGQKQRVALARALVTEPKILLLDEPLSALDAHLKVRMQSVLSN 189 Query: 183 LQQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGESN 242 LQ+ LGITFV+VTH EA +M+D + +M+ G+I Q GTP +IY EP N FVA F+G +N Sbjct: 190 LQKDLGITFVYVTHSMSEAFSMADRVVIMSRGQIEQIGTPEEIYREPHNRFVAEFLGSAN 249 Query: 243 ILPGTM---IED--YLVEFNG-----KRFEAVDGGMKPNEPVEVVIRPEDLRITLPEEGK 292 I G + ED + V + G + E + + + V ++ E+++++LP+ G+ Sbjct: 250 IFDGVVEGPAEDGGWRVSYEGGETVLDKSELAEA--RKGQAVTFIVSAENMQLSLPDSGQ 307 Query: 293 --LQVKVDTQLFRGVHYEIIAYDELGNEWMIHSTRKAI------VGEEIGLDFEPEDIHI 344 + V + F G + G E + T + + G I + + P+ H+ Sbjct: 308 PGIAASVAGEEFIGGTAMVFLETATGQELKVQKTHEELSQLDLHAGSRIIVHWAPDSCHV 367 Query: 345 M 345 + Sbjct: 368 L 368 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: 330 Number of extensions: 11 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: 376 Length adjustment: 30 Effective length of query: 355 Effective length of database: 346 Effective search space: 122830 Effective search space used: 122830 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 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