Alignments for a candidate for gguA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Dinoroseobacter shibae DFL-12

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  295 bits (756), Expect = 2e-84
 Identities = 175/487 (35%), Positives = 281/487 (57%), Gaps = 16/487 (3%)

Query: 6   LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65
           +++R ITK + GV AL++V+  V+ GE   L GENG+GKSTL+K++SGV PA    G + 
Sbjct: 10  IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATA--GTVQ 67

Query: 66  YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNG-VISWQQTFNRT 124
             G          S   G+++I Q+ +L P LS+AENI    ++++   +  ++   +  
Sbjct: 68  IAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIA 127

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
           R  L ++G++   +  +  + V ++QLV I +AL+   +L+I+DEPT +L E +   L  
Sbjct: 128 RAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQG 187

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
           ++   + +G+  I ++HKL EV +V++++ VLR+G   K  +    E     +  +M GR
Sbjct: 188 IIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGK--KVAEGPASEFDTQSLTYHMTGR 245

Query: 245 DLEDRYPPRDVPIG-ETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
           D+ +  PP DV  G +T+++V+                DI+  +R GEV+GI GL+G GR
Sbjct: 246 DVPE-VPPSDVAAGAQTLMQVQGLGKAGS-------FSDISFDLRTGEVLGITGLLGCGR 297

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           T  A ++FG        G +L+DG PV +   + A  A + YV EDR   GL L+ +IL 
Sbjct: 298 TSVAKALFGLVTPD--AGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILR 355

Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423
           N  +  L   +    +D     K ASD+  RL++++  +     +LSGGNQQ+V L++WL
Sbjct: 356 NVAVGRLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWL 415

Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483
              P VLIL+ P+ G+DVG+K +I+ II +LA +G GV++IS ++PELL  C R+ VM E
Sbjct: 416 SRAPRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMRE 475

Query: 484 GRIVAEL 490
           GRI+  L
Sbjct: 476 GRIIDAL 482



 Score = 61.6 bits (148), Expect = 6e-14
 Identities = 56/222 (25%), Positives = 100/222 (45%), Gaps = 9/222 (4%)

Query: 280 LHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAI 339
           L  ++ TV+ GE V +AG  G+G++     + G        G V I G+       R + 
Sbjct: 25  LDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPA--TAGTVQIAGQEHVTLNPRISA 82

Query: 340 DAGLAYVTEDRKHL-GLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIR 398
            AG+  + +D      L + +NI   T L+    + K   + DI   + A D   R+ ++
Sbjct: 83  AAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIA--RAALD---RIGVQ 137

Query: 399 SSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADG 458
              +      L    +Q V + + L S   ++I+DEPT  +       +  II  L  +G
Sbjct: 138 ID-LDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIRMLKEEG 196

Query: 459 KGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESI 500
             V+ +S ++ E+L   +++ V+  G+ VAE P  E   +S+
Sbjct: 197 VAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSL 238



 Score = 57.0 bits (136), Expect = 2e-12
 Identities = 46/238 (19%), Positives = 107/238 (44%), Gaps = 26/238 (10%)

Query: 2   ANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYE 61
           A T+++++ + K      +  +++  ++ GE+  + G  G G++++ K L G+       
Sbjct: 259 AQTLMQVQGLGKA----GSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDA-- 312

Query: 62  GEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN--------- 112
           G I  +G+      + D +   +      +  VP   + E +FL   +  N         
Sbjct: 313 GSILVDGSPV---PLGDPQAASLA----RIGYVPEDRLTEGLFLSQSILRNVAVGRLDAH 365

Query: 113 ---GVISWQQTFNRTRELLKKVGLKESP-ETLITDIGVGKQQLVEIAKALSKSVKLLILD 168
              G +          + L+++ +K    E  +  +  G QQ V +A+ LS++ ++LIL+
Sbjct: 366 TSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILN 425

Query: 169 EPTASLNESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLD 226
            P+  ++      + +++ E   +G+  I+I+  L E+     ++ V+R+G  +  L+
Sbjct: 426 GPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALE 483


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: 540
Number of extensions: 26
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: 498
Length adjustment: 34
Effective length of query: 478
Effective length of database: 464
Effective search space:   221792
Effective search space used:   221792
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources