Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_4628 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4628 Length = 358 Score = 126 bits (316), Expect = 1e-33 Identities = 99/299 (33%), Positives = 144/299 (48%), Gaps = 41/299 (13%) Query: 12 AVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71 AVA + +P++ + + I ++ L ALG+N++VGY G + LG AF AVGAY Sbjct: 34 AVAFVAVPMLASDYFFRAILIP--FVIMSLAALGVNVLVGYCGQISLGSGAFMAVGAYG- 90 Query: 72 ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 A NF P L + + L A FFG + G P+L+++G YLA+ Sbjct: 91 --------AYNFFVRLPGLP------LIPALILGGLCATFFGILFGLPSLRVKGLYLAVA 136 Query: 132 TLG---FGE--IIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSV 186 TL F + +RI LD P SV V L+VFG I S Sbjct: 137 TLAAQFFSDWMFLRIRWFTLDTPSG------------SVSV------SNLQVFGMPIESA 178 Query: 187 TLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGAS 246 T Y L ++VV ++ L IGR WMAIR+ ++AA +GI KL AF + + Sbjct: 179 TSKYLFCLAILVVMALMAKNLVRGAIGREWMAIRDMDVAASVIGIRPMYAKLSAFAVSSF 238 Query: 247 FGGVSGAMFG-AFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVL 304 GV+G ++ + G P +FS+ S ++ MV++GG+G I G GA + LP L Sbjct: 239 IIGVAGGLWAFVYLGAWEPGAFSVDMSFRLLFMVIIGGMGSIMGSFFGAAFIVVLPIAL 297 Lambda K H 0.328 0.144 0.430 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: 340 Number of extensions: 21 Number of successful extensions: 4 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: 358 Length of database: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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