Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF249 PGA1_c02610 putative high-affinity branched-chain amino acid transport ATP-binding protein LivG
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Phaeo:GFF249 Length = 255 Score = 193 bits (491), Expect = 3e-54 Identities = 104/259 (40%), Positives = 157/259 (60%), Gaps = 9/259 (3%) Query: 13 TLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMIT 72 +LL++EH ++KFGG++A+ND SF + G++ A++GPNGAGK+TVFN I+ FY+P G ++ Sbjct: 2 SLLEIEHATLKFGGVVAVNDLSFSVEEGEVYAIVGPNGAGKSTVFNLISRFYQPHSGRLS 61 Query: 73 FNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTI 132 F+ + Q + + D I ARTFQNI LF TVL+NLLV +H + Sbjct: 62 FDGRDLLQSKADAVADLGI------ARTFQNIELFDHATVLQNLLVGRHRHRRSTLMEEL 115 Query: 133 LGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192 V +R A+E ++ DL D LPYG ++ +E+ RA+ +GP L Sbjct: 116 FFTPRVRREERRHRAAVEEV---IDFLDLQAYRDKMIAGLPYGVRKVVELGRALASGPRL 172 Query: 193 LCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKIS 252 L LDEPA+GL+ E+ + + IR + G ++L++EHDM +V +SD V+ L G K++ Sbjct: 173 LLLDEPASGLSVEETRDMRWWIDDIRKQMGITVLMVEHDMGLVSSVSDRVLALADGAKLA 232 Query: 253 DGTPDHVKNDPRVIAAYLG 271 +GTP V+ +P VI AYLG Sbjct: 233 EGTPAEVQANPAVIEAYLG 251 Lambda K H 0.318 0.136 0.386 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: 185 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: 292 Length of database: 255 Length adjustment: 25 Effective length of query: 267 Effective length of database: 230 Effective search space: 61410 Effective search space used: 61410 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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