GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Salinicoccus carnicancri Crm

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_017547633.1 C792_RS0101285 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_000330705.1:WP_017547633.1
          Length = 387

 Score =  219 bits (559), Expect = 8e-62
 Identities = 130/375 (34%), Positives = 207/375 (55%), Gaps = 17/375 (4%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M  +++E++ K +  G      V + ++ I  G    ++GPSG GK+T LR+IAGLE+ T
Sbjct: 1   MAEMKLESIKKTYDNGPA---VVHDFNLEIYDGEFIVLVGPSGCGKSTTLRMIAGLEDIT 57

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G  Y     ++  R   + P+ R IAMVFQN+ALYP+M+V+DN+AF LKL KVPK +I+
Sbjct: 58  DGDFY-----IAGKRMNDVEPKNRDIAMVFQNYALYPHMSVYDNMAFGLKLRKVPKPEIK 112

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +V++ +E LGL+  L+R PK LSGGQ QR A+ RA+V++  V L+DEP SNLDA++R  
Sbjct: 113 ERVEKAAEILGLTDFLDRKPKALSGGQRQRVALGRAIVREANVFLMDEPLSNLDAKLRVQ 172

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            RA + K+ +  K TT+ V+HD  +   +A +  V+  G   Q+GTP E+Y++P    +A
Sbjct: 173 MRAEITKLHKRLKTTTIYVTHDQTEALTMATRIVVMNEGDIMQVGTPKEVYDFPENVFVA 232

Query: 241 RLTGE--INLIQAKIIENNAIIANLKVPLNNMELK-----GQSN--IVIGLRPDDLTLSD 291
           +  G   +N+  A+I +   +I N ++ +   + +     G  N  +  G+RP+D+    
Sbjct: 233 QFIGSPAMNIFDAEIKDGKLVIGNTEITIPEAKRRMLIDEGYDNKALKFGIRPEDIREEA 292

Query: 292 TLLDKYIDMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNK 351
             ++  +         VS   G   ++ S +  +     VDA   L  G         NK
Sbjct: 293 VFVESALASAFKAEVKVSELLGSEIMLYSELEGQEFISRVDARNELNPGDVVKFAFDMNK 352

Query: 352 VKIFDLNGSNLITSK 366
              FD+     I++K
Sbjct: 353 GHFFDMYSGERISTK 367


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: 328
Number of extensions: 10
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: 387
Length adjustment: 30
Effective length of query: 341
Effective length of database: 357
Effective search space:   121737
Effective search space used:   121737
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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