GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PA5503 in Pseudomonas stutzeri RCH2

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component

Query= TCDB::Q9HT70
         (335 letters)



>lcl|FitnessBrowser__psRCH2:GFF139 Psest_0139 ABC-type histidine
           transport system, ATPase component
          Length = 257

 Score =  172 bits (437), Expect = 6e-48
 Identities = 99/251 (39%), Positives = 142/251 (56%), Gaps = 15/251 (5%)

Query: 2   IEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGR 61
           +E  ++HK Y     ++  L+   L  + G +  ++G SG+GKST LR IN LE P  G 
Sbjct: 8   LEIRNLHKRYG----DLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHEGE 63

Query: 62  ILVEGE----------DVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAG 111
           ILV GE          D+ A D + L R R  +G +FQ+FNL    T+ DNI    R   
Sbjct: 64  ILVAGEQLKLKRDKQGDLVAADGKQLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRRVL 123

Query: 112 GFSRAEVDARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSA 171
           G S+AE       LLA+VG++D    YP QLSGGQ+QR  IAR LA +P ++L DE TSA
Sbjct: 124 GQSKAEATEVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183

Query: 172 LDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFL 231
           LDP+    VL ++  +  E + T++L+THEM+  ++V  +V  +  G + EQG    VF 
Sbjct: 184 LDPEMVQEVLAVIRSLAEEGR-TMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVFD 242

Query: 232 HPQHPTTRRFV 242
           +PQ    ++F+
Sbjct: 243 NPQSARCKQFM 253


Lambda     K      H
   0.322    0.138    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: 204
Number of extensions: 9
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: 335
Length of database: 257
Length adjustment: 26
Effective length of query: 309
Effective length of database: 231
Effective search space:    71379
Effective search space used:    71379
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: 48 (23.1 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