GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Azohydromonas australica DSM 1124

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_043458758.1 H537_RS42805 ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000430725.1:WP_043458758.1
          Length = 527

 Score =  226 bits (576), Expect = 2e-63
 Identities = 157/492 (31%), Positives = 258/492 (52%), Gaps = 13/492 (2%)

Query: 6   LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65
           L++ +ITK +P V A  +V+L V+ GEIHA++GENGAGKSTLMK++ G       +G + 
Sbjct: 6   LQLAHITKRYPSVVANSDVSLTVQPGEIHAVLGENGAGKSTLMKIIYGSVKPD--QGTVM 63

Query: 66  YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125
           ++G   +     ++  +GI ++ Q  +L   L++AEN++LG        ++  +      
Sbjct: 64  FDGTPVHIANPKEARALGISMVFQHFSLFDTLTVAENVWLG----LGNHLTLSEVAGGIE 119

Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185
               + GL   P   +  + VG+ Q VEI +AL  S KLLILDEPT+ L     E L  +
Sbjct: 120 AKAAEYGLDIDPSRPVHTLSVGEMQRVEIIRALLGSPKLLILDEPTSVLTPQAVERLFVV 179

Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGRD 245
           L +   +G + + I+HKL+E+R++    TVLR+G    T  C+    S   + R M+G +
Sbjct: 180 LRKLAAEGCSILYISHKLHEIRELCTACTVLRNGKV--TGACNPSMESNASLSRMMIGSE 237

Query: 246 LEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTE 305
                     P G  +L V+  +   +       LH+I + VR GEVVGIAG+ G G+ E
Sbjct: 238 PPALEHHARQP-GAVVLNVQGLSLPREDLFGVN-LHNIALDVRAGEVVGIAGVSGNGQRE 295

Query: 306 FAMSVFGKSYGHRITGDVL-IDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364
           F  ++ G+    R   D + + GK V      +    GL +V E+R   G V   ++  N
Sbjct: 296 FLYALSGED--RRSDPDAIRLSGKSVGRLGPVQRRRLGLHFVPEERLGRGAVPTLSLAQN 353

Query: 365 TTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424
             L     +     ID     + A+D  +R  +++ G   +  +LSGGN QK ++ + + 
Sbjct: 354 LLLTRTDALRTGGWIDVKAMHRQAADIISRFNVKAGGPTSQAKSLSGGNLQKFIVGREID 413

Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484
           + P +LI+ +PT G+DVGA  +I   I     +G  VL++S E+ EL   CDR++V+ +G
Sbjct: 414 AKPKLLIISQPTWGVDVGAAAQIRGEILARRDEGCAVLVVSEELDELFEICDRLHVIAKG 473

Query: 485 RIVAELPKGEAS 496
           ++   + + +A+
Sbjct: 474 QLSPSIDRAQAT 485



 Score = 76.3 bits (186), Expect = 3e-18
 Identities = 58/226 (25%), Positives = 105/226 (46%), Gaps = 12/226 (5%)

Query: 282 DINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDA 341
           D+++TV+ GE+  + G  GAG++     ++G     +  G V+ DG PV ++  ++A   
Sbjct: 23  DVSLTVQPGEIHAVLGENGAGKSTLMKIIYGSVKPDQ--GTVMFDGTPVHIANPKEARAL 80

Query: 342 GLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSG 401
           G++ V +   H  L     +  N  L    G+     + ++     A      L I  S 
Sbjct: 81  GISMVFQ---HFSLFDTLTVAENVWL----GLGNHLTLSEVAGGIEAKAAEYGLDIDPS- 132

Query: 402 IFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGV 461
             +    LS G  Q+V + + L  +P +LILDEPT  +   A   ++ ++ +LAA+G  +
Sbjct: 133 --RPVHTLSVGEMQRVEIIRALLGSPKLLILDEPTSVLTPQAVERLFVVLRKLAAEGCSI 190

Query: 462 LMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRS 507
           L IS ++ E+   C    V+  G++         S  S+ R ++ S
Sbjct: 191 LYISHKLHEIRELCTACTVLRNGKVTGACNPSMESNASLSRMMIGS 236



 Score = 60.1 bits (144), Expect = 2e-13
 Identities = 49/229 (21%), Positives = 106/229 (46%), Gaps = 25/229 (10%)

Query: 21  LENVNLKVKEGEIHALVGENGAGKSTLMKVLSG---------VYPAGTYEGEIHYEGAVR 71
           L N+ L V+ GE+  + G +G G+   +  LSG         +  +G   G +   G V+
Sbjct: 270 LHNIALDVRAGEVVGIAGVSGNGQREFLYALSGEDRRSDPDAIRLSGKSVGRL---GPVQ 326

Query: 72  NFRAINDSEDIGIIIIHQEL---ALVPLLSIAENIFLGNEVA--SNGVISWQQTFNRTRE 126
             R       +G+  + +E      VP LS+A+N+ L    A  + G I  +    +  +
Sbjct: 327 RRR-------LGLHFVPEERLGRGAVPTLSLAQNLLLTRTDALRTGGWIDVKAMHRQAAD 379

Query: 127 LLKKVGLKES-PETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185
           ++ +  +K   P +    +  G  Q   + + +    KLLI+ +PT  ++   +  +   
Sbjct: 380 IISRFNVKAGGPTSQAKSLSGGNLQKFIVGREIDAKPKLLIISQPTWGVDVGAAAQIRGE 439

Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISE 234
           ++  R++G   ++++ +L+E+ ++ D++ V+  G    ++D  Q  I++
Sbjct: 440 ILARRDEGCAVLVVSEELDELFEICDRLHVIAKGQLSPSIDRAQATITQ 488


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: 518
Number of extensions: 29
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 512
Length of database: 527
Length adjustment: 35
Effective length of query: 477
Effective length of database: 492
Effective search space:   234684
Effective search space used:   234684
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 Apr 09 2024. 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