Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate AO353_21860 AO353_21860 methionine ABC transporter ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21860 Length = 328 Score = 191 bits (484), Expect = 5e-53 Identities = 115/314 (36%), Positives = 174/314 (55%), Gaps = 5/314 (1%) Query: 9 LKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVV 68 L V EL+ N + V V ++F++ EI + GESG GK+ A+ LL P + Sbjct: 6 LHVEELSVIAHNGERDVTLVDRLSFDLAEGEILGLVGESGSGKTMACRALMRLLPSPSLR 65 Query: 69 LRGH-VYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GV 126 ++G V L K++L + + +R +R + + Q LDP+ +IG+Q+ H G Sbjct: 66 VQGKAVQLAGKNLLQLDEAGMRAIRGRRLGMIFQNPSSHLDPLMRIGEQIGEGIRLHQGA 125 Query: 127 NVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTT 184 + EAR E L V +P V+ Y HE SGGMRQR +IA ++ NP ++I DEPTT Sbjct: 126 SKREARAQAIEVLRQVGIPDPPRRVDSYAHEFSGGMRQRAMIAVALACNPQVLIADEPTT 185 Query: 185 GLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEII 244 LDV VQ +IL+ L ++ Q G+S+++I+HD+ ++ D + +MYAG + E GSK E++ Sbjct: 186 ALDVTVQAQILRLLLDLRDQRGLSIILITHDLGVVAQTCDSIAVMYAGRLCEHGSKHELL 245 Query: 245 KRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLN 304 RP HPYT LI P+ L +I G PPL L +P+ C F RC + +C+ L Sbjct: 246 VRPRHPYTAGLIDCQPASSVGHAMLRTIAGQPPL-LDALPSGCSFNPRCLQQGSQCTMLL 304 Query: 305 PALGDIMDGHKARC 318 P L + +G + C Sbjct: 305 PDLQIMAEGQRVAC 318 Score = 146 bits (369), Expect = 1e-39 Identities = 92/243 (37%), Positives = 138/243 (56%), Gaps = 12/243 (4%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTS----GKII-LLGKDV--- 429 + V+ +SF+L +G I LVG SG GK+ + L ++ S GK + L GK++ Sbjct: 22 VTLVDRLSFDLAEGEILGLVGESGSGKTMACRALMRLLPSPSLRVQGKAVQLAGKNLLQL 81 Query: 430 SEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVL 489 E G+R + + MIFQ+P S LDP + + + +H+ S K + + IEVL Sbjct: 82 DEAGMRAIRGRR--LGMIFQNPSSHLDPLMRIGEQIGEGIRLHQGAS-KREARAQAIEVL 138 Query: 490 KNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNL 549 + VG+ P + + Y HE SGG RQR IA A A P+VL+ADEP + LD +++A IL L Sbjct: 139 RQVGIPDPPRRVDSYAHEFSGGMRQRAMIAVALACNPQVLIADEPTTALDVTVQAQILRL 198 Query: 550 IKKFK-KNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIE 608 + + + G+SI+ ITHD+ V D I V+Y GR+ E G+ +E++ P H YT LI+ Sbjct: 199 LLDLRDQRGLSIILITHDLGVVAQTCDSIAVMYAGRLCEHGSKHELLVRPRHPYTAGLID 258 Query: 609 AVP 611 P Sbjct: 259 CQP 261 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: 470 Number of extensions: 18 Number of successful extensions: 8 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: 328 Length adjustment: 33 Effective length of query: 584 Effective length of database: 295 Effective search space: 172280 Effective search space used: 172280 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