Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 140 bits (353), Expect = 2e-38 Identities = 86/225 (38%), Positives = 139/225 (61%), Gaps = 13/225 (5%) Query: 20 LIRIEGLNKHYGA----FHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQG 75 ++ IE ++K Y + VL DI+L V+ G+ I + GPSGSGK+TL+ L+ A G Sbjct: 3 ILSIENVSKIYQSGSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSG 62 Query: 76 SIQVDGIDLAATTREA-AQVRS-DIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAE 133 S+ ++G L + + A VRS +IG +FQ+F L P ++ L+N ++ P ++ RKDA+ Sbjct: 63 SVALNGHRLEGLSEDQRAAVRSQEIGFIFQNFQLLPTLTALEN-VMVPLELK--KRKDAK 119 Query: 134 ERARMYLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAE 193 ++A L +VG+ + YP+QLSGG+QQRV+IARA +P+I+ DEPT LD E E Sbjct: 120 QKATELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTE-TGE 178 Query: 194 VLDVLV--QLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIED 236 +++ L+ G T++ VTH+ A + R++ ++GG+I E+ Sbjct: 179 LIETLIFDLNKALGTTLILVTHDTDLAAK-TNRIIHIKGGKIQEE 222 Lambda K H 0.322 0.137 0.395 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: 146 Number of extensions: 8 Number of successful extensions: 3 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: 260 Length of database: 225 Length adjustment: 23 Effective length of query: 237 Effective length of database: 202 Effective search space: 47874 Effective search space used: 47874 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: 46 (22.3 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