Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate AO356_07270 AO356_07270 peptide ABC transporter ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07270 Length = 322 Score = 192 bits (489), Expect = 1e-53 Identities = 113/316 (35%), Positives = 177/316 (56%), Gaps = 6/316 (1%) Query: 7 SLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPG 66 SLL++ L + + + V ++ V E+ AI GESG GKS MA+ GL+++PG Sbjct: 2 SLLEIKNLNVRFGDATAVPV-VDGLDLSVEKGEVLAIVGESGSGKSVTMMALMGLIEHPG 60 Query: 67 VVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-G 125 +V + K++L ++ + R++ K+ V Q M AL+P +G Q+ H Sbjct: 61 IVTADALNFDGKNMLKLSNRQRRQIVGKDLAMVFQDPMTALNPSYTVGFQIEEVLRLHLK 120 Query: 126 VNVEEARKLIKEKLELVDLPYNVVNM--YPHELSGGMRQRVVIATSILLNPSLIILDEPT 183 ++ + ARK E LE V++P M YPH+LSGGM QRV IA +I P L+I DEPT Sbjct: 121 MSGKAARKRAIELLEKVEIPGAASRMDAYPHQLSGGMSQRVAIAMAIAGEPKLLIADEPT 180 Query: 184 TGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEI 243 T LDV +Q +I+ L +Q++ + LV+I+HD++++ + RV +MYAG+ VE+G ++ Sbjct: 181 TALDVTIQAQIMDLLLALQKEQDMGLVLITHDLAVVAETAQRVCVMYAGQAVEVGQVPQL 240 Query: 244 IKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTL 303 P+HPY+ L++++P E+L ++PG P + P C RCP+ + C Sbjct: 241 FDIPAHPYSEALLAAIPEHSMGAERLATLPGIVPGRYDR-PQGCLLSPRCPYVQDNCRQQ 299 Query: 304 NPALGDIMDGHKARCF 319 PAL D ARCF Sbjct: 300 RPAL-DAKSNSLARCF 314 Score = 148 bits (374), Expect = 3e-40 Identities = 85/241 (35%), Positives = 142/241 (58%), Gaps = 7/241 (2%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVSEYG 433 + V+ + ++KG + A+VG SG GKS L G+I+ T+ + GK++ + Sbjct: 19 VPVVDGLDLSVEKGEVLAIVGESGSGKSVTMMALMGLIEHPGIVTADALNFDGKNMLKLS 78 Query: 434 VRNSMWYK-ENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNV 492 R +++ M+FQDP ++L+P +TV + +E L +H K+S K + IE+L+ V Sbjct: 79 NRQRRQIVGKDLAMVFQDPMTALNPSYTVGFQIEEVLRLHLKMSGK-AARKRAIELLEKV 137 Query: 493 GLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKK 552 + + YPH+LSGG QRVAIA A A EPK+L+ADEP + LD +++A I++L+ Sbjct: 138 EIPGAASRMDAYPHQLSGGMSQRVAIAMAIAGEPKLLIADEPTTALDVTIQAQIMDLLLA 197 Query: 553 F-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 K+ + ++ ITHD+A V A + V+Y G+ VE G ++ P+H Y++ L+ A+P Sbjct: 198 LQKEQDMGLVLITHDLAVVAETAQRVCVMYAGQAVEVGQVPQLFDIPAHPYSEALLAAIP 257 Query: 612 D 612 + Sbjct: 258 E 258 Lambda K H 0.319 0.138 0.391 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: 493 Number of extensions: 26 Number of successful extensions: 7 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: 617 Length of database: 322 Length adjustment: 32 Effective length of query: 585 Effective length of database: 290 Effective search space: 169650 Effective search space used: 169650 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 (21.7 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