Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate YP_004141854.1 Mesci_2669 binding-protein-dependent transport system inner membrane protein
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >NCBI__GCF_000185905.1:YP_004141854.1 Length = 282 Score = 193 bits (490), Expect = 4e-54 Identities = 99/245 (40%), Positives = 156/245 (63%), Gaps = 1/245 (0%) Query: 3 ARARWM-LGLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKEGWLLFTEYGFIKDIGMT 61 AR+R++ + +A FV W T G V P FL SP ++A + L + D+ + Sbjct: 31 ARSRFLVIAVAVFVGLGLAWWAATGLGLVKPIFLPSPGSVAMQIAKLAADGTLWLDLKAS 90 Query: 62 IWRVVGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEA 121 ++R+ GF++A+ +++P+G+ +G+++ EA EP + F RY+P AF+PL ILWAG G++ Sbjct: 91 MYRISIGFLIASALSIPIGVLIGSFRSWEAAIEPLVDFIRYMPVVAFVPLSILWAGTGDS 150 Query: 122 QKILVIFIGSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAETL 181 QK L+IFIG+ FQ LM+ V D + TLG + I+TR+++P A P I +TL Sbjct: 151 QKFLIIFIGTFFQQVLMIMDNVKRVPADFIGLGRTLGLPDRKILTRIVVPSALPGIWDTL 210 Query: 182 RLVLGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKAL 241 R+ LGWAWT++++AEL+ ++SG+G+ IT SQ T II I+++GL+GL++D KAL Sbjct: 211 RISLGWAWTWLVLAELVAATSGLGYRITVSQRYFQTNTIIGYILLLGLLGLITDQVMKAL 270 Query: 242 NHRLF 246 LF Sbjct: 271 EKVLF 275 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: 245 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: 282 Length adjustment: 25 Effective length of query: 227 Effective length of database: 257 Effective search space: 58339 Effective search space used: 58339 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