GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Pseudomonas fluorescens GW456-L13

Align ATPase (characterized, see rationale)
to candidate PfGW456L13_446 Cystine ABC transporter, ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_446
          Length = 251

 Score =  228 bits (581), Expect = 9e-65
 Identities = 124/247 (50%), Positives = 163/247 (65%), Gaps = 7/247 (2%)

Query: 21  MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80
           MI  E + K +  Q   L G+ L V+ GEVV ++GPSGSGK+TFLR LN LE    G I 
Sbjct: 1   MIVVEKLTKQFKGQI-VLNGIDLEVKEGEVVAIIGPSGSGKTTFLRCLNFLEEPTSGRIK 59

Query: 81  I------EGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQA 134
           +          L+  +  +  +RQ VG VFQ FNLFPH T L+N++  P+ V++ P A A
Sbjct: 60  VGDIEVDTSRPLNQQQSLVRRLRQHVGFVFQNFNLFPHRTALENVIEGPIVVKKTPHADA 119

Query: 135 EATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVR 194
            A  ++LL +V +A + D YP +LSGGQQQRVAIARALAM+P ++LFDEPTSALDPE+V 
Sbjct: 120 VALGKKLLAKVGLAGKEDAYPRRLSGGQQQRVAIARALAMEPEVILFDEPTSALDPELVG 179

Query: 195 EVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAK 254
           EVL  +R LA E  TM++ THE+GFAR+VA+RVV    G IVE+      F  P+ +R K
Sbjct: 180 EVLATIRGLAEEKRTMVIVTHEMGFARDVANRVVFFDKGVIVEQGEAKALFANPKEERTK 239

Query: 255 QFLAQIL 261
           QFL++ L
Sbjct: 240 QFLSKFL 246


Lambda     K      H
   0.321    0.134    0.387 

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: 208
Number of extensions: 8
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: 261
Length of database: 251
Length adjustment: 24
Effective length of query: 237
Effective length of database: 227
Effective search space:    53799
Effective search space used:    53799
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: 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