Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate YP_004141812.1 Mesci_2627 binding-protein-dependent transport system inner membrane protein
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >NCBI__GCF_000185905.1:YP_004141812.1 Length = 288 Score = 176 bits (446), Expect = 5e-49 Identities = 84/241 (34%), Positives = 137/241 (56%) Query: 9 LGLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKEGWLLFTEYGFIKDIGMTIWRVVGG 68 LG ++ + W T G V FL P ++ + + + + ++ V+ G Sbjct: 47 LGFMVWIAVIGGWFALTYSGAVKEMFLPRPESVLSTTISMALDGSLWEHVFASVQVVLIG 106 Query: 69 FVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEAQKILVIF 128 FVL++++AVPLG+ MG Y+ ++A EP ++F RYLP ++F+PL ILW GIG Q++ VI Sbjct: 107 FVLSSIVAVPLGLTMGTYRIVQAVLEPLVNFIRYLPVTSFVPLFILWIGIGIEQRVAVIV 166 Query: 129 IGSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAETLRLVLGWA 188 G FQ +M+A + +RDLV AAYTLG V ++ P P + + LR+ +GWA Sbjct: 167 FGVFFQQLVMIADSARSVQRDLVNAAYTLGTKRGDTVFHIVFPATLPSVLDVLRVTMGWA 226 Query: 189 WTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKALNHRLFAW 248 WTY++VAEL+ + SG+G++ + I I +IG++GL +D F+ + + W Sbjct: 227 WTYLVVAELVAARSGLGYISLKAMRGFQVDVIFMAIAMIGILGLCTDQLFRGIRRLVAPW 286 Query: 249 S 249 + Sbjct: 287 A 287 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: 224 Number of extensions: 13 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: 288 Length adjustment: 25 Effective length of query: 227 Effective length of database: 263 Effective search space: 59701 Effective search space used: 59701 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 24 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