Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 164 bits (415), Expect = 5e-45 Identities = 117/324 (36%), Positives = 166/324 (51%), Gaps = 31/324 (9%) Query: 5 LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64 L++ G+ K +G VLR +D+ + GEF+ ++G SG GK+TL++++AGL +P GE Sbjct: 4 LELKGVAKSYGASS----VLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGE 59 Query: 65 IRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALE--MRKMPKPERQKRIDEV 122 + + GK V G P DR + VFQSY+L P L+V NI A++ M K ER+ R+ + Sbjct: 60 VLLRGKPVDG-PGADRGV--VFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKY 116 Query: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182 M+ +SH +RRPS+LSGG RQRVA+ RALA P + L DEPLS LDA R +++ EI+ Sbjct: 117 IGMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIE 176 Query: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242 + + T + +T+D EA+ L RI + G G P N P A P Sbjct: 177 AIWEQEKKTVILITNDVDEALLLADRIIPLNPGPGATFG-PSFKVNLPRPRDRAAVNSDP 235 Query: 243 TMNLLRGAVT----------GGQFGIQGAALNLAP-----PPSSANEVLLGVRPEHLVMQ 287 LR VT GG+ G N+AP PP + E P+ V Sbjct: 236 DFKRLRAEVTEYLMAVGVERGGESGETRILPNVAPISFGGPPKAYREAGQVNNPDRYVE- 294 Query: 288 ETAPWRGRVSVVEPTGPDTYVMVD 311 RV + PT +VD Sbjct: 295 -----FSRVKKIYPTPKGPLTVVD 313 Score = 123 bits (308), Expect = 1e-32 Identities = 71/220 (32%), Positives = 123/220 (55%), Gaps = 7/220 (3%) Query: 5 LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64 ++ + + K + + V+ D+ + GEF+ L+G SGCGKST+L + AGL + +EG Sbjct: 293 VEFSRVKKIYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGG 352 Query: 65 IRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAA 124 + + G+ V P D A+VFQ+ +L+P L+ N+ ++ R P +R+D V+ Sbjct: 353 VILDGREVSEAGP---DRAVVFQAPSLFPWLTALQNVALGVD-RVYPHASPAERLDIVSY 408 Query: 125 MLQ---ISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEI 181 L+ + +D++ S +S G RQRV + RA A P+L L DEP LD+ R E++ + Sbjct: 409 YLERVGLGDSMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVL 468 Query: 182 KRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLG 221 + + +T++ VTHD EA+ L ++ +M G ++G Sbjct: 469 MEVWTRTRVTAICVTHDVDEAILLADKVVMMTNGPNARIG 508 Lambda K H 0.318 0.135 0.388 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: 458 Number of extensions: 21 Number of successful extensions: 6 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: 355 Length of database: 553 Length adjustment: 32 Effective length of query: 323 Effective length of database: 521 Effective search space: 168283 Effective search space used: 168283 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: 51 (24.3 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