GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Pseudomonas stutzeri RCH2

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>FitnessBrowser__psRCH2:GFF16
          Length = 278

 Score =  263 bits (672), Expect = 3e-75
 Identities = 137/254 (53%), Positives = 179/254 (70%), Gaps = 1/254 (0%)

Query: 3   EATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQG 62
           +A P +    + KRYG+L VL G+ L   +G+ ++I+G SGSGKST LR +  LE   +G
Sbjct: 20  QAQPLVRFAGVTKRYGELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGIDEG 79

Query: 63  QILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRV 122
            I V GE L      +G LV A+++ + R+R ++G VFQ+FNL+PHM+ L NV+EAP +V
Sbjct: 80  VIEVDGEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQV 139

Query: 123 LGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTS 182
           LG SKAEA   AE LLA VG+ DK   +PAQLSGGQQQR AIAR LAM+PKV+LFDE TS
Sbjct: 140 LGLSKAEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTS 199

Query: 183 ALDPEMVQEVLNVIRALAE-EGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVF 241
           ALDPE+  EVLNVIR L E    TML+VTH+M FAR+ +  V F HQG + EQG+P ++F
Sbjct: 200 ALDPELCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDELF 259

Query: 242 ENPQSARCKQFMSS 255
            NPQ  R ++F+S+
Sbjct: 260 NNPQEERTREFLSA 273


Lambda     K      H
   0.317    0.133    0.367 

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: 199
Number of extensions: 5
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: 257
Length of database: 278
Length adjustment: 25
Effective length of query: 232
Effective length of database: 253
Effective search space:    58696
Effective search space used:    58696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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