Aligments for a candidate for potD in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments 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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources