Align ABC transporter (characterized, see rationale)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 227 bits (578), Expect = 5e-64 Identities = 131/284 (46%), Positives = 172/284 (60%), Gaps = 11/284 (3%) Query: 11 KQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDL 70 ++ G + VSL++ AG F +GPSGCGK+TLLRL+AG D GD+ I G R+ND+ Sbjct: 12 RRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIRGERMNDV 71 Query: 71 EPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRK 130 P R V MVFQ AL+P M+V DNI++GLK K R+R+ + + + L L R Sbjct: 72 PPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQVGLPDLEHRN 131 Query: 131 PKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYV 190 P+ELSGGQRQRVA+ R + EP +LL DEPL LD LR QM+ E+ L + G+T +Y+ Sbjct: 132 PQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQKQFGTTFVYI 191 Query: 191 THDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARL---- 246 THDQ EAM ++D++ V+ GR +QV P ELY PA+ FVAGF+G N LS L Sbjct: 192 THDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGD--NNRLSGELVSVR 249 Query: 247 QTPGETSLVD-TLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSL 289 + E L D LV G + S NL AG L IRPE + L Sbjct: 250 DSLAELRLDDGVLVQGRVA----SDNLQAGHRAELYIRPESLVL 289 Lambda K H 0.320 0.137 0.394 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: 322 Number of extensions: 16 Number of successful extensions: 2 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: 381 Length of database: 362 Length adjustment: 30 Effective length of query: 351 Effective length of database: 332 Effective search space: 116532 Effective search space used: 116532 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 (21.8 bits) S2: 49 (23.5 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