GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01113 in Desulfovibrio vulgaris Hildenborough

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

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



>lcl|MicrobesOnline__882:206505 DVU1070 branched chain amino acid
           ABC transporter, ATP-binding protein
          Length = 524

 Score =  211 bits (537), Expect = 5e-59
 Identities = 152/483 (31%), Positives = 245/483 (50%), Gaps = 25/483 (5%)

Query: 14  PFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLV 73
           P + + G+ K F  V A   ++L    G+I  LLGENG GKSTL+ I+SG    D G + 
Sbjct: 33  PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIH 92

Query: 74  IEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVL 133
           ++G      S  +AL AGI  VYQ   L+ +M+VAENV L    A     L+     RV+
Sbjct: 93  VDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGAW----LSPVHMSRVV 148

Query: 134 AATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQK 193
           A  AAR        G     +  +  L +  RQ V I + +  +++ +I+DEPT  LT  
Sbjct: 149 AELAARY-------GLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPG 201

Query: 194 EVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT-KAQIS 252
           E + L   L  +   G  ++F+SHK+ E  A+  E+ +LR G+ + +   +E   +A+++
Sbjct: 202 ETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELA 261

Query: 253 ELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNE 312
             M GR +  E   E     D VL V G    G    +SF++  GE+  + G+  +G+ E
Sbjct: 262 NRMVGREVILEVAAEPLEPGDRVLHVDGLAGDG-LKGLSFEVRKGEVFAIAGVAGNGQRE 320

Query: 313 LARALAGVAPAQSGDVLLDG---QQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDN 369
           L   + G+     G+V L G   +Q   + P   ++  + Y+PEDR      L   + DN
Sbjct: 321 LVECVTGLRRPAEGEVELLGIPWRQFFTKAP---RQGGLAYIPEDRQGLATCLSLDLVDN 377

Query: 370 -VITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRW 428
            ++TA     R  F  +DR  A A A   + E  +     + P +SLSGGN Q++++GR 
Sbjct: 378 FLLTARGCFTRGPF--LDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGRE 435

Query: 429 LAIDPRVLILHGPTVGVDVGSKDIIY-RIMQRLSQRGIGIILISDDLPELLQNCDRILMM 487
               P +++   PT G+D+ + + ++ R+++  S    G++L+S DL E+L   DR+ +M
Sbjct: 436 FYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSH--AGVLLVSGDLNEVLALADRVAVM 493

Query: 488 KKG 490
            +G
Sbjct: 494 YRG 496



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 63/228 (27%), Positives = 109/228 (47%), Gaps = 19/228 (8%)

Query: 289 DVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRI 348
           D++  +  G I  + G   +G++ L   L+G     +G + +DG+ +  R+P DA +  I
Sbjct: 52  DITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGI 111

Query: 349 GYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGV 408
           G V +  +   L     + +NV+           GQ     +     + V EL  A  G+
Sbjct: 112 GMVYQHFM---LVDSMTVAENVL----------LGQSGAWLSPVHMSRVVAELA-ARYGL 157

Query: 409 D----KPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRG 464
           D      V  LS G +QRV I + L  D RVLIL  PT  +  G  + ++  + R+++ G
Sbjct: 158 DIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENG 217

Query: 465 IGIILISDDLPELLQNCDRILMMKKGHVSAEYRADEL-SEADLYHALL 511
             I+ IS  + E+L   D I ++++G V  E+   E+  EA+L + ++
Sbjct: 218 KAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMV 265


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: 586
Number of extensions: 28
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 515
Length of database: 524
Length adjustment: 35
Effective length of query: 480
Effective length of database: 489
Effective search space:   234720
Effective search space used:   234720
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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