GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potD in Desulfovibrio vulgaris Hildenborough

Align spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein PotD (characterized)
to candidate 209024 DVU0095 polyamine ABC transporter, periplasmic polyamine-binding protein

Query= CharProtDB::CH_088339
         (348 letters)



>MicrobesOnline__882:209024
          Length = 345

 Score =  346 bits (887), Expect = e-100
 Identities = 166/340 (48%), Positives = 231/340 (67%)

Query: 6   RHLLAAGALALGMSAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETM 65
           R L     L L    A + +   L  +NW+EYVP  +L++FTKETGIKV+Y+TYESNE M
Sbjct: 3   RLLATVVMLLLWTGVAVSAEPKVLNVFNWSEYVPQTVLDRFTKETGIKVVYTTYESNEAM 62

Query: 66  YAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDY 125
           YAK+K  +   YD+VVPSTY++D MRK+G++ KID++KLTN++NLDP +L++PFDP N++
Sbjct: 63  YAKIKLLRGKGYDIVVPSTYFIDMMRKDGLLAKIDRAKLTNYANLDPRVLHQPFDPQNEF 122

Query: 126 SIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGN 185
           S+PY+WG T + VN   VDP +++SW DL++PE+KG ++L+DD R+ F +AL+ LGYS N
Sbjct: 123 SVPYMWGNTGLMVNRKVVDPATISSWNDLFRPEFKGGVILSDDLRDTFGIALKALGYSVN 182

Query: 186 TTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDV 245
           +T   EI+AAY  L KL P+V  F+       ++  EV  GM WNG AF+A      +  
Sbjct: 183 STSEAEIKAAYEWLLKLKPSVRVFDVTATKQAFIAEEVKGGMSWNGDAFIAMNENPDLAF 242

Query: 246 VWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLS 305
           V+PKEG   W+DSLAIP  A++K+ A K I+FLLRPD+AK   E   Y TPNLAA+K+L 
Sbjct: 243 VYPKEGLPLWVDSLAIPIGAEHKDNAHKFIDFLLRPDIAKLCVEEYNYSTPNLAAQKILD 302

Query: 306 PEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLK 345
              A  +   P    +KN E+ N VG A  +YE+Y++ LK
Sbjct: 303 ARHAQSRATSPTDADLKNSEFTNGVGKALDVYEKYWEMLK 342


Lambda     K      H
   0.314    0.132    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: 444
Number of extensions: 13
Number of successful extensions: 1
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: 348
Length of database: 345
Length adjustment: 29
Effective length of query: 319
Effective length of database: 316
Effective search space:   100804
Effective search space used:   100804
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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