Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate Ac3H11_2553 Cell division transporter, ATP-binding protein FtsE (TC 3.A.5.1.1)
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2553 Length = 265 Score = 225 bits (573), Expect = 8e-64 Identities = 126/247 (51%), Positives = 162/247 (65%), Gaps = 7/247 (2%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIV 60 ++ I+ + K +G VL +V +V+VV GPSGSGKST ++C N LE + G V + Sbjct: 18 IVRIRGLRKAFGSHVVLNGIDFDVLPSQVVVVIGPSGSGKSTFLRCCNGLEQPEGGSVEI 77 Query: 61 DGTSIAD-----PKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASK 115 G ++ P +L LR VGMVFQ F LFPHLS++DN+T+ K+ G S++EA + Sbjct: 78 CGRTLVQDGRMLPDHDLNALREEVGMVFQSFNLFPHLSVLDNVTLGPRKLRGLSRKEAEE 137 Query: 116 KALQLLERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEV 175 +A LL +VGL+ A P LSGGQ+QRVAIARALAM+P VMLFDEPTSALDPE+V EV Sbjct: 138 RAQALLTKVGLAHKAPAMPASLSGGQKQRVAIARALAMEPRVMLFDEPTSALDPELVGEV 197 Query: 176 LDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDITARSDRAQ 235 L VM LA EGMTMM VTHEM FAR+V D V+ MD G IIE F + T +R + Sbjct: 198 LQVMKLLASEGMTMMVVTHEMDFAREVGDVVVVMDGGGIIEAGAPATIFTNPT--QERTR 255 Query: 236 HFLEKIL 242 FL+ +L Sbjct: 256 SFLQAVL 262 Lambda K H 0.321 0.135 0.390 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: 194 Number of extensions: 6 Number of successful extensions: 2 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: 244 Length of database: 265 Length adjustment: 24 Effective length of query: 220 Effective length of database: 241 Effective search space: 53020 Effective search space used: 53020 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 (21.9 bits) S2: 47 (22.7 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