GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5405 in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate HSERO_RS19240 HSERO_RS19240 arginine ABC transporter ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



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

 Score =  275 bits (703), Expect = 6e-79
 Identities = 134/240 (55%), Positives = 178/240 (74%)

Query: 14  IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73
           +I++  V+KWYG F VL D + +VK+G+ +V+CGPSGSGKST I+ +N LE  Q+G I V
Sbjct: 1   MIELNNVSKWYGSFQVLTDCSTSVKKGDVVVVCGPSGSGKSTLIKTVNGLEPFQKGTITV 60

Query: 74  DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133
           DGV + +    +  +R  +GMVFQ+F LFPHL+I +N T+  + V    K +A E  + Y
Sbjct: 61  DGVSVGDPKTNLSKLRARIGMVFQNFELFPHLSIRENLTIGQIKVLGRSKEEATEKGLKY 120

Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193
           L+RV +     K+PGQLSGGQQQRVAIARAL M P  MLFDEPTSALDPEM+ EVLD M+
Sbjct: 121 LDRVGLLAHKDKFPGQLSGGQQQRVAIARALSMDPIAMLFDEPTSALDPEMINEVLDVMV 180

Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQIL 253
           GLA++GMTM+ VTHEMGFAR VANRV+FMDKG +VE  A ++FF  P+++R + FL++I+
Sbjct: 181 GLAQEGMTMMVVTHEMGFARKVANRVVFMDKGVVVEDCAKDEFFAQPRSERARDFLAKII 240


Lambda     K      H
   0.322    0.137    0.407 

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: 185
Number of extensions: 4
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: 254
Length of database: 242
Length adjustment: 24
Effective length of query: 230
Effective length of database: 218
Effective search space:    50140
Effective search space used:    50140
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 (21.9 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, the preprint on GapMind for carbon sources, 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