GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aatP in Herbaspirillum seropedicae SmR1

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate HSERO_RS19240 HSERO_RS19240 arginine ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_16275
         (244 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19240 HSERO_RS19240 arginine
           ABC transporter ATP-binding protein
          Length = 242

 Score =  379 bits (973), Expect = e-110
 Identities = 187/244 (76%), Positives = 212/244 (86%), Gaps = 2/244 (0%)

Query: 1   MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVVV 60
           MI + NV+KWYG FQVLTDCST VKKG+V+VVCGPSGSGKSTLIK VN LEPFQKG + V
Sbjct: 1   MIELNNVSKWYGSFQVLTDCSTSVKKGDVVVVCGPSGSGKSTLIKTVNGLEPFQKGTITV 60

Query: 61  DGTSIADPKTDLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120
           DG S+ DPKT+L KLR+R+GMVFQ+FELFPHL+I ENLTI QIKVLGRSKEEAT+KGL+ 
Sbjct: 61  DGVSVGDPKTNLSKLRARIGMVFQNFELFPHLSIRENLTIGQIKVLGRSKEEATEKGLKY 120

Query: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180
           L+RVGL AH  K PGQLSGGQQQRVAIARAL+MDPI MLFDEPTSALDPEM+NEVLDVMV
Sbjct: 121 LDRVGLLAHKDKFPGQLSGGQQQRVAIARALSMDPIAMLFDEPTSALDPEMINEVLDVMV 180

Query: 181 QLANEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARSDRAQHFLDK 240
            LA EGMTMM VTHEMGFARKVA+RV+FMD+G ++EDC K+EFF     RS+RA+ FL K
Sbjct: 181 GLAQEGMTMMVVTHEMGFARKVANRVVFMDKGVVVEDCAKDEFFA--QPRSERARDFLAK 238

Query: 241 ILQH 244
           I+ H
Sbjct: 239 IITH 242


Lambda     K      H
   0.321    0.136    0.394 

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: 268
Number of extensions: 9
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: 244
Length of database: 242
Length adjustment: 23
Effective length of query: 221
Effective length of database: 219
Effective search space:    48399
Effective search space used:    48399
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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