GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Caldicellulosiruptor hydrothermalis 108

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_041723256.1 CALHY_RS00570 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000166355.1:WP_041723256.1
          Length = 505

 Score =  396 bits (1017), Expect = e-114
 Identities = 222/513 (43%), Positives = 333/513 (64%), Gaps = 18/513 (3%)

Query: 1   MANT--ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAG 58
           MA T  ILEM  ITK FPGVKAL+NV +K+K G +HAL+GENGAGKSTLMK L G+Y   
Sbjct: 1   MAKTEYILEMNGITKEFPGVKALDNVTVKIKRGTVHALLGENGAGKSTLMKCLFGIYKLD 60

Query: 59  TYEGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGN----EVASNGV 114
           +  GEI  +G   +     D+  +GI +IHQEL  V   ++ ENI+LG      V     
Sbjct: 61  S--GEIILDGQHVHINNPIDAIKLGISMIHQELQPVNQRNVMENIWLGRFPRVSVGPFKF 118

Query: 115 ISWQQTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASL 174
           ++ ++ +  T+ LL+K+ +   P+ ++  + V K QL+EIAKA+S + K++++DEPT+SL
Sbjct: 119 VNHKKMYEDTKALLQKLEIDVDPKAIVGHLSVSKVQLIEIAKAVSYNSKVIVMDEPTSSL 178

Query: 175 NESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISE 234
            E++ E L  ++ + +++G++ I I+HKL E+ ++AD++T++RDG  V +      E++ 
Sbjct: 179 TENEVEHLFRIIRDLKSKGVSIIYISHKLEEIFEIADEVTIMRDGKVVGSWSI--SELTP 236

Query: 235 DVIIRNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVG 294
           D++I NMVGR + DR+P +     E IL+V+N  +      D +   +++  +RKGE++G
Sbjct: 237 DMMIANMVGRQMSDRFPQKTNKPSEVILKVENLTSV-----DPKSFKNVSFELRKGEILG 291

Query: 295 IAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLG 354
           I GL+GA RTE   ++FG        G + I GK V +   + AI   +A +TEDRK  G
Sbjct: 292 IGGLVGAQRTELIEAIFGLRSIKE--GKIFIKGKEVIIKNPQDAIRNKIALLTEDRKLTG 349

Query: 355 LVLNDNILHNTTLANLAG-VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGN 413
           ++   NIL NTTLA+L   ++   +++D K +    +F   LRI++     +  NLSGGN
Sbjct: 350 IIPELNILENTTLASLRKYLNGFGLLNDKKRLLDTQNFIDILRIKTPSYKAQIKNLSGGN 409

Query: 414 QQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLG 473
           QQKV++++WL + P++L+LDEPTRGIDVGAK+EIY +INQLA +GK ++MISSEMPELLG
Sbjct: 410 QQKVLIARWLLTEPEILLLDEPTRGIDVGAKFEIYNLINQLATEGKSIIMISSEMPELLG 469

Query: 474 NCDRIYVMNEGRIVAELPKGEASQESIMRAIMR 506
             DRI VM EGR+   L + EA++E IM+   R
Sbjct: 470 MSDRILVMCEGRVSGILERNEATEEEIMKLATR 502


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: 641
Number of extensions: 39
Number of successful extensions: 12
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: 505
Length adjustment: 34
Effective length of query: 478
Effective length of database: 471
Effective search space:   225138
Effective search space used:   225138
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.

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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