GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Pseudomonas stutzeri RCH2

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>FitnessBrowser__psRCH2:GFF4241
          Length = 335

 Score =  166 bits (419), Expect = 8e-46
 Identities = 101/251 (40%), Positives = 137/251 (54%), Gaps = 14/251 (5%)

Query: 15  LLEIRDLHKQYGP----LEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGG 70
           ++E   +HK Y      +  L+   L +  G V  LIG SG+GK+TLLR +N LEE  GG
Sbjct: 1   MIEFHQVHKTYRTGGRDVPALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGG 60

Query: 71  QILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVK 130
           +IL++GE +   + +G R         + R   GM FQ FNL    T   NV + L    
Sbjct: 61  RILVNGEDVTALDADGLR---------RFRQRVGMIFQHFNLLMSKTVADNVAMPLRLAG 111

Query: 131 KLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSA 190
              + E        LERVGL E    YP QLSGGQ+QRV IARA+A  PS++L DE TSA
Sbjct: 112 IRSRREIDARVAALLERVGLKEHARKYPAQLSGGQKQRVGIARALATEPSILLCDEATSA 171

Query: 191 LDPELVGEVLSVIKGL-AEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFE 249
           LDP+    VL ++  +  E  +T++L+THEM     V D++  M+ G I EQGP  E+F 
Sbjct: 172 LDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVFL 231

Query: 250 RPQSPRLAEFL 260
            P+ P    F+
Sbjct: 232 HPKHPTTQRFV 242


Lambda     K      H
   0.319    0.135    0.379 

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: 213
Number of extensions: 9
Number of successful extensions: 4
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: 265
Length of database: 335
Length adjustment: 26
Effective length of query: 239
Effective length of database: 309
Effective search space:    73851
Effective search space used:    73851
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: 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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