Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3200 Length = 604 Score = 233 bits (593), Expect = 1e-65 Identities = 136/266 (51%), Positives = 176/266 (66%), Gaps = 7/266 (2%) Query: 16 PVAQPV-TAAI----KLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLR 70 PVA P T A+ ++ + G+ KRYG EVLK V+L G V ++G SGSGKST+LR Sbjct: 340 PVAVPRWTGALNRGGEVTIHGVSKRYGALEVLKDVTLTVLPGSVTVILGPSGSGKSTLLR 399 Query: 71 CINFLEQPDAGVITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVL 130 IN LE+ D G I +DG I RQ ++ + R + MVFQ+FNL+ H+TVL Sbjct: 400 SINHLERVDGGFIAIDGELIGYRQDADALYELGENDILKRRVDVGMVFQNFNLFPHLTVL 459 Query: 131 ENITMAPRRVLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAME 190 ENI AP V ++ AEAE A L +VGL + A YP LSGGQQQRVAIARALA++ Sbjct: 460 ENIVEAPVTVRKLARAEAEALALELLARVGLSDK-AHSYPRQLSGGQQQRVAIARALALK 518 Query: 191 PEIILFDEPTSALDPELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRV 250 P+++LFDEPTSALDPELVGEVL VI+ LA G T+++VTHE+GFAR+V+ V+F+ QGRV Sbjct: 519 PKVLLFDEPTSALDPELVGEVLDVIKELARTGTTLVIVTHEIGFAREVADTVVFMEQGRV 578 Query: 251 EEHG-DARILDQPNSERLQQFLSNRL 275 E G A++ QP+ R FL+ L Sbjct: 579 VETGTPAKVFSQPDHPRTAAFLAKVL 604 Lambda K H 0.319 0.133 0.372 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: 376 Number of extensions: 20 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: 276 Length of database: 604 Length adjustment: 31 Effective length of query: 245 Effective length of database: 573 Effective search space: 140385 Effective search space used: 140385 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: 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