Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate HSERO_RS15940 HSERO_RS15940 peptide ABC transporter substrate-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__HerbieS:HSERO_RS15940 Length = 334 Score = 190 bits (483), Expect = 7e-53 Identities = 111/322 (34%), Positives = 181/322 (56%), Gaps = 10/322 (3%) Query: 5 MDSLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKY 64 M LL V L ++G + V ++F+V E+ + GESGCGKS ++A+ GLL Sbjct: 1 MSVLLDVKNLKVDLPTENGMLHAVRGIDFQVRRGEMLCLVGESGCGKSMTSLALMGLLPR 60 Query: 65 PGVVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH 124 H+ D+ + ++L +LR K + Q M +L+P +G+Q+ A + Sbjct: 61 KAQCSADHILFDGVDLHGMPDKQLMQLRGKRMAMIFQEPMTSLNPSYTLGNQLCEAMLQQ 120 Query: 125 -GVNVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILDE 181 GV+ EAR+ L + + + YPH+LSGG+RQRV+IA S++ NP LII DE Sbjct: 121 PGVSRAEARERALYLLHRTGISNAEDRLRQYPHQLSGGLRQRVMIAMSLMCNPDLIIADE 180 Query: 182 PTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKE 241 PTT LDV +Q +IL+ ++ +Q++ G +++ I+HD+ ++ I+DRV +MYAG++VE Sbjct: 181 PTTALDVTIQAQILRMIRELQQEFGAAVIFITHDLGVVSRIADRVAVMYAGQVVETTDVA 240 Query: 242 EIIKRPSHPYTYLLISSLPSLVKR--REKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEK 299 ++ +P HPYT L++ +P K L +IPG P ++ +V + C F +RC K + Sbjct: 241 QLFAQPRHPYTQGLLNCIPVRGKTLPGSHLQAIPGVVPSLVGQV-SGCAFRNRCA-KADS 298 Query: 300 CSTLNPAL---GDIMDGHKARC 318 +P + G + H+ARC Sbjct: 299 GCERDPQMVQQGSVTAPHQARC 320 Score = 144 bits (363), Expect = 6e-39 Identities = 85/259 (32%), Positives = 151/259 (58%), Gaps = 12/259 (4%) Query: 370 KNLILSEP-----INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMI----QQTSG 420 KNL + P ++AV + F++++G + LVG SG GKS + L G++ Q ++ Sbjct: 8 KNLKVDLPTENGMLHAVRGIDFQVRRGEMLCLVGESGCGKSMTSLALMGLLPRKAQCSAD 67 Query: 421 KIILLGKDVSEYGVRNSMWYK-ENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKD 479 I+ G D+ + M + + + MIFQ+P +SL+P +T+ + +L VS + Sbjct: 68 HILFDGVDLHGMPDKQLMQLRGKRMAMIFQEPMTSLNPSYTLGNQLCEAMLQQPGVS-RA 126 Query: 480 QLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLD 539 + + + +L G+ E L +YPH+LSGG RQRV IA + P +++ADEP + LD Sbjct: 127 EARERALYLLHRTGISNAEDRLRQYPHQLSGGLRQRVMIAMSLMCNPDLIIADEPTTALD 186 Query: 540 ASLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNP 598 +++A IL +I++ ++ G ++++ITHD+ V+ IAD + V+Y G++VE + ++ + P Sbjct: 187 VTIQAQILRMIRELQQEFGAAVIFITHDLGVVSRIADRVAVMYAGQVVETTDVAQLFAQP 246 Query: 599 SHEYTKRLIEAVPDPYKTI 617 H YT+ L+ +P KT+ Sbjct: 247 RHPYTQGLLNCIPVRGKTL 265 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: 425 Number of extensions: 23 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: 617 Length of database: 334 Length adjustment: 33 Effective length of query: 584 Effective length of database: 301 Effective search space: 175784 Effective search space used: 175784 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