GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE in Phaeobacter inhibens BS107

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF250 PGA1_c02620 high-affinity branched-chain amino acid transport ATP-binding protein LivF

Query= TCDB::P73650
         (240 letters)



>lcl|FitnessBrowser__Phaeo:GFF250 PGA1_c02620 high-affinity
           branched-chain amino acid transport ATP-binding protein
           LivF
          Length = 257

 Score =  199 bits (507), Expect = 3e-56
 Identities = 104/225 (46%), Positives = 152/225 (67%), Gaps = 3/225 (1%)

Query: 14  YVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLG 73
           +   +  ++G++ S+  G++VTV+G NGAGKSTL KTI G++ P +G + F GE I G  
Sbjct: 14  FYGPIMAIRGVSLSVQAGQIVTVLGANGAGKSTLLKTISGIMDPEKGSVSFNGEEIQGEE 73

Query: 74  SDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDR--IYTMFPKLAQRRN 131
             +IVRRG+ +VP+   VF  L+V ENL +GA+  +   +  +DR  ++  FP LA+RR+
Sbjct: 74  PHRIVRRGIVHVPEGREVFPLLSVEENLTLGAYTRRDQAEIERDRQMVFDYFPILAERRH 133

Query: 132 QRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINA-TGKAII 190
           Q AGTLSGG++QMLA+GR LML P ++LLDEPS  LSP+LV+++F  +K +N   G  ++
Sbjct: 134 QEAGTLSGGQQQMLAIGRGLMLRPRIMLLDEPSLGLSPLLVQEIFGILKRLNRDEGVTMM 193

Query: 191 LVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
           LVEQNA+ AL +A  GYV+E GR  ++GS   L+    +   YLG
Sbjct: 194 LVEQNARIALELAHVGYVMEIGRIVMDGSADRLMESEDIKSFYLG 238


Lambda     K      H
   0.320    0.139    0.393 

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: 176
Number of extensions: 4
Number of successful extensions: 3
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: 240
Length of database: 257
Length adjustment: 24
Effective length of query: 216
Effective length of database: 233
Effective search space:    50328
Effective search space used:    50328
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, 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