Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein
Query= SwissProt::P54537 (240 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3200 Length = 604 Score = 251 bits (642), Expect = 2e-71 Identities = 131/249 (52%), Positives = 174/249 (69%), Gaps = 10/249 (4%) Query: 2 IKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIK 61 + + +SK +G EVLK+++ T+ G V ++GPSGSGKST LR +N LE+ +GG I I Sbjct: 356 VTIHGVSKRYGALEVLKDVTLTVLPGSVTVILGPSGSGKSTLLRSINHLERVDGGFIAID 415 Query: 62 ----------DTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQ 111 D + + LK R ++GMVFQ+F+LFPH TVLENI+ APV V+K ++ Sbjct: 416 GELIGYRQDADALYELGENDILKRRVDVGMVFQNFNLFPHLTVLENIVEAPVTVRKLARA 475 Query: 112 AAQEKAEDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEM 171 A+ A +LL +VGL +K + YP +LSGGQ+QRVAIARALA+ P ++LFDEPTSALDPE+ Sbjct: 476 EAEALALELLARVGLSDKAHSYPRQLSGGQQQRVAIARALALKPKVLLFDEPTSALDPEL 535 Query: 172 VKEVLQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKR 231 V EVL V+KEL TG T+VIVTHE+GFA+EVAD V+FM+QG +VE G P + F P R Sbjct: 536 VGEVLDVIKELARTGTTLVIVTHEIGFAREVADTVVFMEQGRVVETGTPAKVFSQPDHPR 595 Query: 232 AQDFLEKIL 240 FL K+L Sbjct: 596 TAAFLAKVL 604 Lambda K H 0.317 0.134 0.368 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: 306 Number of extensions: 8 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: 240 Length of database: 604 Length adjustment: 30 Effective length of query: 210 Effective length of database: 574 Effective search space: 120540 Effective search space used: 120540 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 (21.6 bits) S2: 50 (23.9 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