Alignments for a candidate for H281DRAFT_01113 in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Paraburkholderia bryophila 376MFSha3.1

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate H281DRAFT_02704 H281DRAFT_02704 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Burk376:H281DRAFT_02704
          Length = 511

 Score =  334 bits (857), Expect = 4e-96
 Identities = 188/494 (38%), Positives = 296/494 (59%), Gaps = 11/494 (2%)

Query: 4   QEVSSAPLSQ--PFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKII 61
           +E   AP+++  P L + G+ K F GV ALRGVSL  + G +  ++GENG GKS+L+K +
Sbjct: 6   EERERAPVNRSVPLLRMQGIVKSFPGVKALRGVSLELRAGHVMAIVGENGAGKSSLVKTL 65

Query: 62  SGAQPPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHE 121
           SGA  PDEG + I+GVP AR     A+ AG+  +YQ+LSL+ +M+VAEN+ L   +   +
Sbjct: 66  SGAYEPDEGTIEIDGVPLAR-GTNAAIDAGVAVIYQELSLINDMTVAENLFL-GRMPARK 123

Query: 122 GRLARTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFV 181
           G + +    R     A  AL  VGL     +    +  LPL  RQLV +A+AIA +A+ +
Sbjct: 124 GFIMQ----REANQLAREALARVGLDSVPPWMR--LGDLPLNKRQLVEVAKAIARDARIL 177

Query: 182 IMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQG 241
           +MDEPT +L  +++ NL AV+  LRA G+ ++F+SH L+E + +    +V+RDG  +   
Sbjct: 178 VMDEPTAALQSQDIVNLYAVVRRLRAAGMGIIFISHHLEEVFELADSAVVMRDGATVGAR 237

Query: 242 PIAEFTKAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILG 301
           P++E+T+A + + M  R+L +    E     D+VL+VR    A    + SFK+  GEI+G
Sbjct: 238 PMSEWTEAALVQAMVARNLESFYPWEPRDYGDVVLEVRNLVSAPLLRNASFKVRAGEIVG 297

Query: 302 VTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLF 361
           + G+  +GR EL + + G  PA  G++L+ G++IA  +P++  RH + Y  EDR  EGL 
Sbjct: 298 IAGIAGAGRTELLKTIFGALPATGGEILIKGKKIANHSPTEGVRHGLVYTSEDRKLEGLV 357

Query: 362 LDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQ 421
           LD  I +N+  + + +L +  G +   R + LA        +    V +  ++LSGGNQQ
Sbjct: 358 LDANIEENIALSSLKALANG-GFVSGARKRKLARDASTRFGVRASSVLQVTRTLSGGNQQ 416

Query: 422 RVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNC 481
           +V++GR  A  P V++L  PT G+DVG+K  IY  M  +++ G  ++++S +LPELL   
Sbjct: 417 KVILGRATATQPVVIMLDEPTRGIDVGAKTEIYAHMVAMARAGGAVVMVSSELPELLGMS 476

Query: 482 DRILMMKKGHVSAE 495
           DR+L+M +G +  E
Sbjct: 477 DRVLVMYRGSIVTE 490



 Score = 75.1 bits (183), Expect = 6e-18
 Identities = 59/215 (27%), Positives = 100/215 (46%), Gaps = 8/215 (3%)

Query: 31  LRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAA 90
           LR  S   + G+I  + G  G G++ L+K I GA P   G+++I+G   A  S  E +  
Sbjct: 283 LRNASFKVRAGEIVGIAGIAGAGRTELLKTIFGALPATGGEILIKGKKIANHSPTEGVRH 342

Query: 91  GIETVYQDLSL---LPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGLP 147
           G+    +D  L   + + ++ EN+AL+S  A   G       +R LA  A+      G+ 
Sbjct: 343 GLVYTSEDRKLEGLVLDANIEENIALSSLKALANGGFVSGARKRKLARDASTRF---GVR 399

Query: 148 GNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRA 207
            +S  Q T    L    +Q V + RA A++   +++DEPT  +       + A +  +  
Sbjct: 400 ASSVLQVT--RTLSGGNQQKVILGRATATQPVVIMLDEPTRGIDVGAKTEIYAHMVAMAR 457

Query: 208 QGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGP 242
            G  V+ VS +L E   +   V+V+  G  + + P
Sbjct: 458 AGGAVVMVSSELPELLGMSDRVLVMYRGSIVTEIP 492



 Score = 70.1 bits (170), Expect = 2e-16
 Identities = 57/237 (24%), Positives = 110/237 (46%), Gaps = 11/237 (4%)

Query: 278 VRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIAL 337
           V+ F        VS +L  G ++ + G   +G++ L + L+G      G + +DG  +A 
Sbjct: 26  VKSFPGVKALRGVSLELRAGHVMAIVGENGAGKSSLVKTLSGAYEPDEGTIEIDGVPLA- 84

Query: 338 RTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQT 397
           R  + A    +  + ++     L  D  + +N+    + +   R G I +  A  LA + 
Sbjct: 85  RGTNAAIDAGVAVIYQEL---SLINDMTVAENLFLGRMPA---RKGFIMQREANQLAREA 138

Query: 398 VKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDII--YR 455
           +  + + +      +  L    +Q V + + +A D R+L++  PT  +   S+DI+  Y 
Sbjct: 139 LARVGLDSVPPWMRLGDLPLNKRQLVEVAKAIARDARILVMDEPTAALQ--SQDIVNLYA 196

Query: 456 IMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALLS 512
           +++RL   G+GII IS  L E+ +  D  ++M+ G         E +EA L  A+++
Sbjct: 197 VVRRLRAAGMGIIFISHHLEEVFELADSAVVMRDGATVGARPMSEWTEAALVQAMVA 253


Lambda     K      H
   0.319    0.135    0.376 

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: 554
Number of extensions: 23
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 515
Length of database: 511
Length adjustment: 35
Effective length of query: 480
Effective length of database: 476
Effective search space:   228480
Effective search space used:   228480
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: 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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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