GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Desulfovibrio vulgaris Miyazaki F

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate 8502041 DvMF_2754 ABC transporter related (RefSeq)

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Miya:8502041
          Length = 238

 Score =  220 bits (561), Expect = 2e-62
 Identities = 117/238 (49%), Positives = 163/238 (68%), Gaps = 4/238 (1%)

Query: 12  LEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITF 71
           LE+ ++H  Y  +V+ L G+N  V+ GE+VT++G NGAGK+T   +I GL+ P  G + F
Sbjct: 3   LELRDLHVKY-GNVEALHGINVHVDEGEIVTILGANGAGKTTTLMSISGLVQPSQGGVYF 61

Query: 72  KGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDS--LQPLKDKIFAM 129
           KGK +  + S+ +VR G+   P+   VF +L+V ENL +GAF  ND   ++  +D IF +
Sbjct: 62  KGKALHEMPSHAVVREGITQSPEGRRVFGTLTVLENLNLGAFTSNDKARIRKTRDWIFEL 121

Query: 130 FPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQI 189
           FPRL +R+ Q AGTLSGGE+QMLA+G+ALM +P +L+LDEPS  L+PILV  +FE V+ I
Sbjct: 122 FPRLLERKDQLAGTLSGGEQQMLAIGRALMGDPKVLLLDEPSLGLAPILVKSIFETVRAI 181

Query: 190 NQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGAGKGH 247
           N+ G  ++LVEQNAR AL++A RGYVLE GR  +      LL +P V + YLG G GH
Sbjct: 182 NKTGMTVVLVEQNARAALKLATRGYVLEVGRVVMEDSAANLLANPDVQDAYLG-GSGH 238


Lambda     K      H
   0.317    0.136    0.377 

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: 167
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: 247
Length of database: 238
Length adjustment: 23
Effective length of query: 224
Effective length of database: 215
Effective search space:    48160
Effective search space used:    48160
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 (21.6 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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