Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate WP_068865628.1 I603_RS12870 cation acetate symporter
Query= reanno::PV4:5209923 (572 letters) >NCBI__GCF_001677335.1:WP_068865628.1 Length = 591 Score = 776 bits (2004), Expect = 0.0 Identities = 396/600 (66%), Positives = 468/600 (78%), Gaps = 37/600 (6%) Query: 1 MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60 MD Q+L YL VG +FALYIGIAIWSRAGST EFYVAGGGV+PV+NGMATAADWMSAASFI Sbjct: 1 MDTQSLIYLFVGASFALYIGIAIWSRAGSTSEFYVAGGGVNPVVNGMATAADWMSAASFI 60 Query: 61 SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120 S+AGI++F GYD SVYLMGWTGGYVLLAL +APYLRKFG+FTVPDFIG RYYS+AAR VA Sbjct: 61 SMAGIIAFTGYDASVYLMGWTGGYVLLALLLAPYLRKFGQFTVPDFIGTRYYSKAARVVA 120 Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180 V+C I + FTYIAGQMRGVG+VFSRFL+V++ TGV IGM +VF Y+VLGGMKGITYTQVA Sbjct: 121 VICLILVSFTYIAGQMRGVGIVFSRFLDVDITTGVVIGMGIVFVYSVLGGMKGITYTQVA 180 Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFS 240 Q+CVLIFA+MVPA F+S M+TG+ +PQ G G+++ DA +G+Y+L+KLD + LGF+ Sbjct: 181 QFCVLIFAYMVPAFFLSFMITGNPVPQFGLGSKVGDA----SGLYVLQKLDLVLTGLGFA 236 Query: 241 QYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTI 300 YT G K MIDVF IT ALM GTAGLPHVIVRFFTVPK DAR+SAGWAL+FIA++YTT Sbjct: 237 AYTAGQKSMIDVFCITLALMVGTAGLPHVIVRFFTVPKASDARLSAGWALIFIALLYTTA 296 Query: 301 PALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGE-- 358 PA+ AF+R+N IE++N AY AP W NWE LI + DKN DG + Y KG+ Sbjct: 297 PAVGAFARLNFIESVNEQ-----AYAQAPAWFTNWEGNDLIAFADKNGDGVMQYRKGDAF 351 Query: 359 --------------------------TNEMKIDRDIMVLATPEIANLPAWVIALVAAGGL 392 NE+ +D+DIMVLA PEI LP WVIALVAAGGL Sbjct: 352 TGKPEFTGETGASGERLVVNPPVTDNANEVYVDQDIMVLANPEIGKLPGWVIALVAAGGL 411 Query: 393 AAALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPG 452 AAALST+AGLLLVIS +VSHDLLK+ F P IS+K ELL AR+AA I +AGY GINPPG Sbjct: 412 AAALSTAAGLLLVISAAVSHDLLKQTFRPAISEKGELLAARLAATAAIGVAGYLGINPPG 471 Query: 453 FVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNPGD 512 +VA VVA AFGLAA+SLFPAI+MGIFS+ MN+EGAIAGMV GL F+ YI++FK V+P Sbjct: 472 WVAQVVAFAFGLAAASLFPAILMGIFSKRMNREGAIAGMVSGLAFTFGYIVWFKLVSPDT 531 Query: 513 NNASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHDH 572 + A+NWLFGISPEGIG++GM INFAVA VS +TAA P + +V+SIR P+GAGEA H Sbjct: 532 STAANWLFGISPEGIGVIGMAINFAVATAVSGITAAPPSEIARLVDSIRVPRGAGEAQVH 591 Lambda K H 0.326 0.140 0.423 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: 1208 Number of extensions: 53 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 572 Length of database: 591 Length adjustment: 36 Effective length of query: 536 Effective length of database: 555 Effective search space: 297480 Effective search space used: 297480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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