Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate PfGW456L13_5057 Dipeptide transport ATP-binding protein DppD (TC 3.A.1.5.2)
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5057 Length = 322 Score = 189 bits (480), Expect = 2e-52 Identities = 112/316 (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 SLLEIKNLNVRFGDKNATPV-VDGLDLQVDKGEVLAIVGESGSGKSVTMMALMGLIEHPG 60 Query: 67 VVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-G 125 +V + K++L + + R++ K+ V Q M AL+P +G Q+ H Sbjct: 61 IVTADALNFDGKNMLKLNNRQRRQIVGKDLSMVFQDPMTALNPSYTVGFQIEEVLRLHLK 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 TALDVTIQAQIMDLLLALQKEQNMGLVLITHDLAVVAETAQRVCVMYAGQAVEVGQVPQL 240 Query: 244 IKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTL 303 P+HPY+ L+ ++P +L ++PG P + P C RCP+ + C Sbjct: 241 FDIPAHPYSEALLKAIPEHSLGASRLSTLPGIVPGRYDR-PQGCLLSPRCPYVKDNCRQQ 299 Query: 304 NPALGDIMDGHKARCF 319 PAL D ARCF Sbjct: 300 RPAL-DQKSNSLARCF 314 Score = 149 bits (377), Expect = 1e-40 Identities = 85/238 (35%), Positives = 142/238 (59%), Gaps = 7/238 (2%) Query: 381 VNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVSEYGVRN 436 V+ + ++ KG + A+VG SG GKS L G+I+ T+ + GK++ + R Sbjct: 22 VDGLDLQVDKGEVLAIVGESGSGKSVTMMALMGLIEHPGIVTADALNFDGKNMLKLNNRQ 81 Query: 437 SMWYK-ENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNVGLK 495 +++ M+FQDP ++L+P +TV + +E L +H K+S K + IE+L+ V + Sbjct: 82 RRQIVGKDLSMVFQDPMTALNPSYTVGFQIEEVLRLHLKMSGK-AARKRAIELLEKVEIP 140 Query: 496 PPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKKF-K 554 + YPH+LSGG QRVAIA A A EPK+L+ADEP + LD +++A I++L+ K Sbjct: 141 GAASRMDAYPHQLSGGMSQRVAIAMAIAGEPKLLIADEPTTALDVTIQAQIMDLLLALQK 200 Query: 555 KNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVPD 612 + + ++ ITHD+A V A + V+Y G+ VE G ++ P+H Y++ L++A+P+ Sbjct: 201 EQNMGLVLITHDLAVVAETAQRVCVMYAGQAVEVGQVPQLFDIPAHPYSEALLKAIPE 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: 491 Number of extensions: 25 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