Alignments for a candidate for H281DRAFT_01113 in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Rhizobium leguminosarum 3841

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_011648977.1 RL_RS33880 sugar ABC transporter ATP-binding protein

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



>NCBI__GCF_000009265.1:WP_011648977.1
          Length = 504

 Score =  347 bits (889), Expect = e-100
 Identities = 198/483 (40%), Positives = 292/483 (60%), Gaps = 9/483 (1%)

Query: 12  SQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGA-QPPDEG 70
           +QP L + G++  F GV AL+ VS     G+++ L GENG GKSTLIK+ISG  +P D  
Sbjct: 11  AQPLLSLRGINMTFGGVKALKNVSFEVLPGEVHCLAGENGSGKSTLIKVISGVYRPADGA 70

Query: 71  QLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDR 130
           ++V +G   + ++   A + GI+ ++QDL+L P MSVAEN+A      T  G   R  + 
Sbjct: 71  EIVFDGETISHMTPAMAQSRGIQIIWQDLALFPEMSVAENIAFQ----TLSGSRPRFVNY 126

Query: 131 RVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSL 190
             + A A  AL  +G+  + +     ++   +A RQ+VAIARA+  EA+ V MDEPT SL
Sbjct: 127 AAIRAIAEEALVRLGVTLDVDRP---LKDFAIAQRQIVAIARALVGEARIVFMDEPTASL 183

Query: 191 TQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQ 250
           TQ E D+L+A++  L A GV V+FVSH+L E   I   + VLRDG  +   P+   T++ 
Sbjct: 184 TQSETDHLLAIVRTLSASGVAVVFVSHRLAEVLDISSRITVLRDGALVGVYPVEGMTQSD 243

Query: 251 ISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGR 310
           I+ELMTGR         +     ++L V   +R G+F D+SF L  GE LGVTGLL SGR
Sbjct: 244 ITELMTGRTFDQNVRARNVSQNPVLLSVGKLSRPGEFEDISFDLRRGETLGVTGLLGSGR 303

Query: 311 NELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNV 370
            ELA  L G+    +G ++L+G+ +   +  +A    + Y+ EDRL+ GL   + I DN+
Sbjct: 304 TELALTLFGMRRPATGTIVLEGRAMRFASNREAIASGVAYLSEDRLSLGLNQPQSIADNL 363

Query: 371 ITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLA 430
           + A ++ +      I   + ++L  + + +L I     D  + +LSGGNQQRV I +WLA
Sbjct: 364 VMASLNRILGG-RLISPEKKRSLVARWIADLGIRIGKQDDAISTLSGGNQQRVAIAKWLA 422

Query: 431 IDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKG 490
            DP+VLIL  PTVGVDVG++  I+ I+ RL++ G+ IILISD++PE+  N DRI+ M+KG
Sbjct: 423 TDPKVLILDAPTVGVDVGARAGIFEIVARLAEAGLAIILISDEVPEVYFNADRIIHMEKG 482

Query: 491 HVS 493
            ++
Sbjct: 483 RIA 485



 Score = 92.0 bits (227), Expect = 4e-23
 Identities = 62/237 (26%), Positives = 123/237 (51%), Gaps = 11/237 (4%)

Query: 275 VLDVRG----FTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGV-APAQSGDVL 329
           +L +RG    F       +VSF++  GE+  + G   SG++ L + ++GV  PA   +++
Sbjct: 14  LLSLRGINMTFGGVKALKNVSFEVLPGEVHCLAGENGSGKSTLIKVISGVYRPADGAEIV 73

Query: 330 LDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTR 389
            DG+ I+  TP+ A+   I  + +D     LF +  + +N+    +S  R RF  ++   
Sbjct: 74  FDGETISHMTPAMAQSRGIQIIWQDL---ALFPEMSVAENIAFQTLSGSRPRF--VNYAA 128

Query: 390 AQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGS 449
            +A+AE+ +  L + T  VD+P++  +   +Q V I R L  + R++ +  PT  +    
Sbjct: 129 IRAIAEEALVRLGV-TLDVDRPLKDFAIAQRQIVAIARALVGEARIVFMDEPTASLTQSE 187

Query: 450 KDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADL 506
            D +  I++ LS  G+ ++ +S  L E+L    RI +++ G +   Y  + ++++D+
Sbjct: 188 TDHLLAIVRTLSASGVAVVFVSHRLAEVLDISSRITVLRDGALVGVYPVEGMTQSDI 244


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: 602
Number of extensions: 29
Number of successful extensions: 10
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: 504
Length adjustment: 34
Effective length of query: 481
Effective length of database: 470
Effective search space:   226070
Effective search space used:   226070
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 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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