Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate HSERO_RS07880 HSERO_RS07880 peptide ABC transporter substrate-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__HerbieS:HSERO_RS07880 Length = 330 Score = 220 bits (561), Expect = 6e-62 Identities = 119/314 (37%), Positives = 191/314 (60%), Gaps = 5/314 (1%) Query: 9 LKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVV 68 L+V L +F +G + V +V+ V I + GESG GKS +I G++ PG + Sbjct: 6 LEVRNLRTHFFTPEGVLPAVDDVSLSVGRGRILGLVGESGSGKSVTGFSILGMVDAPGRI 65 Query: 69 LRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHG-VN 127 + G + + +D++ + + LR+L+ + Q M L+PV K+ QM+ A ++H V+ Sbjct: 66 VGGEILFQGRDLVRMDKTSLRELQGNRIAMIFQDPMMTLNPVLKVEAQMVDAVLAHSKVS 125 Query: 128 VEEARKLIKEKLELVDL--PYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTG 185 ++AR+L ++ L ++ + P + YPH+LSGGMRQRV IA ++L P LII DEPTT Sbjct: 126 RQQARELARDTLGMMGIASPEERLQAYPHQLSGGMRQRVAIAIAMLHKPDLIIADEPTTA 185 Query: 186 LDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIK 245 LDV +Q +IL +++++ RQ G +L+ I+HD+S++ ++D V +MYAG IVE GS + ++ Sbjct: 186 LDVTIQAQILSEVQKLARQHGTALIWITHDLSVVAGLADEVAVMYAGRIVEQGSVDAVLD 245 Query: 246 RPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNP 305 P HPYT LI SLPS +R +L IPG P +L +P +C F RC ++C + P Sbjct: 246 APLHPYTQGLIGSLPSNNRRGARLRQIPGMTPNLL-HLPPTCAFAARCERLSQQC-LVAP 303 Query: 306 ALGDIMDGHKARCF 319 A+ + + H+ RC+ Sbjct: 304 AISEPLPAHRVRCY 317 Score = 158 bits (399), Expect = 4e-43 Identities = 93/238 (39%), Positives = 144/238 (60%), Gaps = 7/238 (2%) Query: 380 AVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVSEYGVR 435 AV+DVS + +G I LVG SG GKS + GM+ G+I+ G+D+ Sbjct: 24 AVDDVSLSVGRGRILGLVGESGSGKSVTGFSILGMVDAPGRIVGGEILFQGRDLVRMDKT 83 Query: 436 NSMWYKEN-VQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNVGL 494 + + N + MIFQDP +L+P V + +L H KVS + Q + L +G+ Sbjct: 84 SLRELQGNRIAMIFQDPMMTLNPVLKVEAQMVDAVLAHSKVS-RQQARELARDTLGMMGI 142 Query: 495 KPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKKF- 553 PE+ L YPH+LSGG RQRVAIA A +P +++ADEP + LD +++A IL+ ++K Sbjct: 143 ASPEERLQAYPHQLSGGMRQRVAIAIAMLHKPDLIIADEPTTALDVTIQAQILSEVQKLA 202 Query: 554 KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 +++G ++++ITHD++ V +ADE+ V+Y GRIVE+G+ V+ P H YT+ LI ++P Sbjct: 203 RQHGTALIWITHDLSVVAGLADEVAVMYAGRIVEQGSVDAVLDAPLHPYTQGLIGSLP 260 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: 468 Number of extensions: 22 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: 330 Length adjustment: 33 Effective length of query: 584 Effective length of database: 297 Effective search space: 173448 Effective search space used: 173448 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