Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate 3607471 Dshi_0884 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Dino:3607471 Length = 360 Score = 217 bits (552), Expect = 8e-61 Identities = 118/296 (39%), Positives = 177/296 (59%), Gaps = 4/296 (1%) Query: 8 LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67 +L + LT + + V V++++ P EI + GESG GKS A+ GLL P Sbjct: 5 VLSIRNLTVDIPTRYAVLRPVDKVSYDIAPGEILGVVGESGAGKSMAGNAVIGLLTPPAH 64 Query: 68 VLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GV 126 + G V+L K I +T E++R++R K+ V Q + +L+P+ +IGDQ+ ++H + Sbjct: 65 ISSGEVWLNGKRIDRLTPEQMRRVRGKDIGMVFQDPLTSLNPLLRIGDQLTETMLAHLPI 124 Query: 127 NVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTT 184 + EA + LE V +P VN YPHE SGGMRQRVVIA ++ PSL+I DEPTT Sbjct: 125 SRAEAEERAVAALEEVGIPAARQRVNSYPHEFSGGMRQRVVIALALCAEPSLVIADEPTT 184 Query: 185 GLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEII 244 LDV VQ +I+ LKR+ R+ G ++++I+HD+ ++ +DRV +MYAG + E+G E++ Sbjct: 185 ALDVSVQAQIIALLKRLCRERGTAVMLITHDMGVIAEAADRVAVMYAGRLAELGPVREVL 244 Query: 245 KRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKC 300 P HPYT+ L+ S P K ++L IPG+ P L ++P C F RCP +KC Sbjct: 245 TAPRHPYTFGLMGSTPLASKGLKRLHQIPGSMP-RLGRLPPGCAFSPRCPRAQDKC 299 Score = 142 bits (358), Expect = 2e-38 Identities = 80/240 (33%), Positives = 135/240 (56%), Gaps = 7/240 (2%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVSEYG 433 + V+ VS+++ G I +VG SG GKS + G++ +SG++ L GK + Sbjct: 22 LRPVDKVSYDIAPGEILGVVGESGAGKSMAGNAVIGLLTPPAHISSGEVWLNGKRIDRLT 81 Query: 434 VRNSMWYK-ENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNV 492 + +++ M+FQDP +SL+P + + +L H +S + + + + L+ V Sbjct: 82 PEQMRRVRGKDIGMVFQDPLTSLNPLLRIGDQLTETMLAHLPIS-RAEAEERAVAALEEV 140 Query: 493 GLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKK 552 G+ + + YPHE SGG RQRV IA A EP +++ADEP + LD S++A I+ L+K+ Sbjct: 141 GIPAARQRVNSYPHEFSGGMRQRVVIALALCAEPSLVIADEPTTALDVSVQAQIIALLKR 200 Query: 553 F-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 ++ G +++ ITHD+ + AD + V+Y GR+ E G EV++ P H YT L+ + P Sbjct: 201 LCRERGTAVMLITHDMGVIAEAADRVAVMYAGRLAELGPVREVLTAPRHPYTFGLMGSTP 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: 532 Number of extensions: 22 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: 360 Length adjustment: 33 Effective length of query: 584 Effective length of database: 327 Effective search space: 190968 Effective search space used: 190968 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