GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Pseudovibrio axinellae Ad2

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  233 bits (594), Expect = 1e-65
 Identities = 163/506 (32%), Positives = 269/506 (53%), Gaps = 25/506 (4%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +L ++NITK F  + A  NVNL +  GEI AL+GENGAGK+TLM +L G Y A   EG +
Sbjct: 10  LLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVAD--EGRV 67

Query: 65  HYE---GAVRNFR--AINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQ 119
                 G + +    A   + + GI ++HQ   L   L+  ENI LG E       S  +
Sbjct: 68  MVRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFARKFSRSK 127

Query: 120 TFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDS 179
              + +EL++  GL+   +  ++ + VG++Q VEI KAL +  ++L+LDEPTA L   +S
Sbjct: 128 ARAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQES 187

Query: 180 EALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTV---KTLDCHQEEISEDV 236
           ++L N L     +GM  I I+HK+ EV   +D++ VLR G  V    T  C + +++E +
Sbjct: 188 DSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELM 247

Query: 237 IIRNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIA 296
           +   +   + E   P      GE IL  K  +A       R+++ ++N+++RKGE++G+A
Sbjct: 248 VGHAVQMAEREPGNP------GEEILVFKGVSA----GEGRELIENVNLSLRKGEIIGLA 297

Query: 297 GLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLV 356
           G+ G G++  A  + G        G V +  +P+  +    AI +G+A + EDR H G+V
Sbjct: 298 GVSGNGQSMLAKVLSGLE--EPTAGAVTLGSQPLKANAA-AAIQSGVARIPEDRHHDGIV 354

Query: 357 LNDNILHNTTLANL--AGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQ 414
              ++  N  L  +      +  ++   +  K A +      IR SG    +  LSGGN 
Sbjct: 355 GAMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNI 414

Query: 415 QKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGN 474
           QK+VL++ L   P +++  +P+RG+DVGA  +++  + +    G GVL+IS ++ EL   
Sbjct: 415 QKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQL 474

Query: 475 CDRIYVMNEGRIVAELPKGEASQESI 500
            DRI V++ G +   +   E  ++ +
Sbjct: 475 SDRIAVIHRGHVSEPMASEELDKKQV 500


Lambda     K      H
   0.316    0.135    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: 600
Number of extensions: 46
Number of successful extensions: 8
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: 512
Length of database: 515
Length adjustment: 35
Effective length of query: 477
Effective length of database: 480
Effective search space:   228960
Effective search space used:   228960
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: 52 (24.6 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