GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Cronobacter condimenti 1330

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_007664567.1 BN137_RS17300 putrescine ABC transporter ATP-binding subunit PotG

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_000319285.1:WP_007664567.1
          Length = 377

 Score =  206 bits (524), Expect = 8e-58
 Identities = 118/317 (37%), Positives = 188/317 (59%), Gaps = 21/317 (6%)

Query: 6   VKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFD 65
           ++N++K F      A+D+V++ I  GE F +LG SG GK+T +R++AG + P+TG++  D
Sbjct: 22  IRNLTKSFDGQH--AVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPTTGQIVLD 79

Query: 66  DRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVA 125
              ++      VPP  R I M+FQ++AL+P++T  +NIAF L   K+ K EI  RVEE+ 
Sbjct: 80  GVDLSH-----VPPYQRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVEEML 134

Query: 126 KILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKE 185
            ++ +       P +LSGGQ+QRVALAR+L K P LLLLDEP   LD ++RD  +  V +
Sbjct: 135 GLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVD 194

Query: 186 VQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245
           +  R+G T ++V+HD  +   +A R+ ++ +GK VQ+G+PE++Y++P +   A  IG +N
Sbjct: 195 ILERVGATCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVN 254

Query: 246 ELEGKV---TNEGVVIGS--LRFPVSVSSDRAI-------IGIRPEDVKLSKDVIKDDSW 293
             +G +     +G++I +  L  P+ V  D ++       + +RPE V L  +   D   
Sbjct: 255 VFDGLLRERREDGLIIDAPGLVHPLKVDPDASVVDGVPVHVALRPEKVMLCDEPPADG-- 312

Query: 294 ILVGKGKVKVIGYQGGL 310
              G G+V  I Y G L
Sbjct: 313 FNFGVGEVVHIAYLGDL 329


Lambda     K      H
   0.319    0.139    0.390 

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: 276
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: 353
Length of database: 377
Length adjustment: 30
Effective length of query: 323
Effective length of database: 347
Effective search space:   112081
Effective search space used:   112081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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