Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate PfGW456L13_1400 Urea carboxylase-related ABC transporter, permease protein
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1400 Length = 267 Score = 191 bits (486), Expect = 1e-53 Identities = 94/240 (39%), Positives = 152/240 (63%), Gaps = 1/240 (0%) Query: 10 GLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKEGWLLFTEYGFIKDIGMTIWRVVGGF 69 GLA+ V+ V +WA + GG V FL +P + + L + + + ++ V+ GF Sbjct: 28 GLAW-VLLVGLWAGLSYGGVVPGMFLPTPGAVVEAAVRLGRDGTLGQHVWASVEVVMVGF 86 Query: 70 VLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEAQKILVIFI 129 ++++++AVPLG+ MG+++ ++AF EP ++F RYLP ++F+PL ILW GIG Q++ VI Sbjct: 87 IVSSLVAVPLGLLMGSFRIVQAFLEPLVNFIRYLPVTSFVPLFILWIGIGLEQRVSVIIF 146 Query: 130 GSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAETLRLVLGWAW 189 G FQ +M+A G +DL+ A+YTLG+ + V V+ P + P + +TLR+ +GWAW Sbjct: 147 GVFFQQLVMIADVSKGISKDLINASYTLGSNRRDAVLHVIAPASLPGVLDTLRVTMGWAW 206 Query: 190 TYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKALNHRLFAWS 249 TY++VAEL+ +SSG+G++ + I I IIGL+GLV+D F+ L R+ AW+ Sbjct: 207 TYLVVAELVAASSGLGYLSLKAMRGFQVDVIFLAIAIIGLLGLVTDQLFRFLRLRITAWA 266 Lambda K H 0.331 0.145 0.456 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: 257 Number of extensions: 11 Number of successful extensions: 1 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: 252 Length of database: 267 Length adjustment: 24 Effective length of query: 228 Effective length of database: 243 Effective search space: 55404 Effective search space used: 55404 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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