GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Pseudomonas fluorescens FW300-N2E2

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate Pf6N2E2_3921 Cystine ABC transporter, ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3921
          Length = 253

 Score =  248 bits (633), Expect = 9e-71
 Identities = 130/248 (52%), Positives = 177/248 (71%), Gaps = 3/248 (1%)

Query: 8   LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEV 67
           +I  ++L K F    VL G+  +I   +V++IIGPSG GK+TFLRCLN LE  S GR++V
Sbjct: 1   MIVVEKLTKQFKGQVVLNGIDLKIEEGEVVAIIGPSGSGKTTFLRCLNFLEEPSSGRIKV 60

Query: 68  AGVDLSGAK-IDQKH--LRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAK 124
             +++ G++ ++Q+   +R+LR +VG VFQ+FNLFPH T L+N+   P+ V +IP  EA+
Sbjct: 61  GDIEIDGSRPLNQQQGLVRRLRQQVGFVFQNFNLFPHRTALENVTEGPQVVKKIPRTEAE 120

Query: 125 DRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGE 184
                 L KVGL  K D YP +LSGGQ+QRVAIAR L M+P ++LFDEPTSALDPELVGE
Sbjct: 121 ALGRKLLAKVGLAGKEDAYPRRLSGGQQQRVAIARALAMEPAVILFDEPTSALDPELVGE 180

Query: 185 VLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRA 244
           VL  ++ LAEE  TM +VTHEM FAR+V+NRV FF++G+I E+G+   +F  PK +R R 
Sbjct: 181 VLATIRDLAEEKRTMVIVTHEMGFARDVANRVVFFDKGVIVEQGEAKALFAAPKEERTRQ 240

Query: 245 FLSRIQSS 252
           FLS+  S+
Sbjct: 241 FLSKFLSA 248


Lambda     K      H
   0.321    0.139    0.397 

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: 6
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: 252
Length of database: 253
Length adjustment: 24
Effective length of query: 228
Effective length of database: 229
Effective search space:    52212
Effective search space used:    52212
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: 46 (22.3 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