GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE in Pseudomonas fluorescens FW300-N2E3

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate AO353_13360 AO353_13360 ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_13360 AO353_13360 ABC
           transporter ATP-binding protein
          Length = 238

 Score =  187 bits (474), Expect = 2e-52
 Identities = 107/229 (46%), Positives = 147/229 (64%), Gaps = 6/229 (2%)

Query: 9   DVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGEN 68
           DVF G    +  L+ ++  I  GE V++IG NGAGKSTL  +IFG    + G+I+++G +
Sbjct: 12  DVFYG---PIQALKKVSLHINEGETVSLIGSNGAGKSTLLMSIFGQPRAAGGQIVYRGVD 68

Query: 69  ITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFL--HQGPTQTLKDRIYTMFPKL 126
           IT   S  I   G+   P+   VF  +TV ENL MG      Q  T+ ++ R++ +FP+L
Sbjct: 69  ITHKSSHYIASNGIAQSPEGRRVFPDMTVEENLLMGTIPIGDQYATEDMQ-RMFELFPRL 127

Query: 127 AQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATG 186
            +RRNQRA T+SGGE+QMLA+ RALM  P LLLLDEPS  L+PI+VK +FA ++ +  TG
Sbjct: 128 KERRNQRAMTMSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFATLRELAGTG 187

Query: 187 KAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
             I LVEQNA  AL ++DR YV+ NG  +L G+G+ LL +  V   YLG
Sbjct: 188 MTIFLVEQNANHALKLSDRAYVMVNGEIRLSGTGKELLVNEEVRNAYLG 236


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: 161
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: 240
Length of database: 238
Length adjustment: 23
Effective length of query: 217
Effective length of database: 215
Effective search space:    46655
Effective search space used:    46655
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.

Links

Downloads

Related tools

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