GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Marinomonas arctica 328

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_111609142.1 DK187_RS20415 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_003259225.1:WP_111609142.1
          Length = 371

 Score =  211 bits (538), Expect = 2e-59
 Identities = 130/374 (34%), Positives = 205/374 (54%), Gaps = 28/374 (7%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M ++++ N+ K F      V  +  + + I  G    ++G SG GK+T LRL++GLE+ T
Sbjct: 1   MASVKLNNIKKRFGN----VDVLHGIDLDIKDGEFVVLIGESGCGKSTLLRLLSGLEDIT 56

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G +Y D+E V+       SP KRGIAMVFQ++ALYP+M VF N+AF LK++   K  + 
Sbjct: 57  EGDLYIDDERVNG-----RSPAKRGIAMVFQSYALYPHMNVFKNMAFGLKISGKDKAFVN 111

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
           NKV E +++L +  +L R P+ELSGGQ QR AI RA+V+DPKV L DEP SNLDA +R  
Sbjct: 112 NKVMEAAKKLKIDHLLERLPRELSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDASLRVQ 171

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  + K+ +E K T + V+HD  +   + +K  V+  G+  Q+G P ++Y +P T  +A
Sbjct: 172 TRVELGKLHQELKATVVYVTHDQVEAMTLGDKIVVMNKGRVEQVGAPLDLYHHPKTQFVA 231

Query: 241 RLTG--EINLIQAKI----IENNAIIAN----LKVPLNNMELKGQSNIVIGLRPDDLTLS 290
              G  ++N + AKI     EN  I+      ++  +++  L     + +GLRP+ + L 
Sbjct: 232 GFIGSPKMNFLNAKIHHSDPENTQIMLESGRVIQASIDSSSLNKGDIVKLGLRPEHIAL- 290

Query: 291 DTLLDKYIDMGIVK--VKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAK 348
                 + D   V+  V L+ +   +  + V    +  + + VD +   + G       +
Sbjct: 291 ------HCDNNTVEGTVTLIEHLGELSYLYVDIGQEGEMVLKVDGDNQHQAGDNITFGIQ 344

Query: 349 PNKVKIFDLNGSNL 362
           PN + +FD  G  L
Sbjct: 345 PNHLYLFDHQGKAL 358


Lambda     K      H
   0.317    0.136    0.374 

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: 323
Number of extensions: 13
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: 371
Length of database: 371
Length adjustment: 30
Effective length of query: 341
Effective length of database: 341
Effective search space:   116281
Effective search space used:   116281
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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