Alignments for a candidate for H281DRAFT_01113 in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Sinorhizobium meliloti 1021

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate SM_b20485 SM_b20485 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__Smeli:SM_b20485
          Length = 509

 Score =  366 bits (939), Expect = e-105
 Identities = 205/505 (40%), Positives = 304/505 (60%), Gaps = 11/505 (2%)

Query: 4   QEVSSAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISG 63
           Q  S+A   +P L +  ++  F GV AL+ VS   Q G+++ L GENGCGKSTLIK+I+G
Sbjct: 8   QSASAASTDKPLLSLRNINMTFGGVKALKNVSFEVQPGEVHCLAGENGCGKSTLIKVITG 67

Query: 64  AQPPDEGQLV-IEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEG 122
              P EG ++  +G  +  +S + A   GI+ ++QDL+L P M+VAEN+A    L    G
Sbjct: 68  VYRPAEGAVIEYDGETYPHMSPVTAQDRGIQVIWQDLALFPEMTVAENIAFHEVL----G 123

Query: 123 RLARTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVI 182
              R  D   +   A  AL  +G+  + +     +++  +A RQ+VAIARA+  EAK V 
Sbjct: 124 GRPRLVDYGRMRRIAVDALGRLGITLDVDLP---LKEYAIAQRQIVAIARALVGEAKLVF 180

Query: 183 MDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGP 242
           MDEPT SLTQ E D+L+ ++ +L A GV V+FVSH+L E   I   + VLRDG  +   P
Sbjct: 181 MDEPTASLTQSETDHLLEIVRSLSASGVAVVFVSHRLAEVLEISSRITVLRDGALVGVYP 240

Query: 243 IAEFTKAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGV 302
            A  T+++I+ELMTG+             Q +VLDVRG TR GQF D+SF +  GE +G+
Sbjct: 241 AAGMTQSKITELMTGKTFDQHVRARPRDDQPVVLDVRGLTRPGQFEDISFTVRRGETVGI 300

Query: 303 TGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFL 362
           TGLL +GR E+A AL G+    +G + +DG+++   +  +A R  + Y+ EDRL+ GL  
Sbjct: 301 TGLLGAGRTEVALALFGMLKPATGTISIDGREVRFGSNREAIRAGVAYLSEDRLSLGLIQ 360

Query: 363 DKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQR 422
            +PI DN++ A +  +    G +   R ++L  + + +L +        + +LSGGNQQR
Sbjct: 361 PQPIADNLVIASLRKILSG-GLLSEDRKRSLVSRWIADLGVKIGHQADAISTLSGGNQQR 419

Query: 423 VLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCD 482
           V I +WLA DP++LIL  PTVGVDVG++  I+ I+ +L++ G+ IILISD++PE+  N D
Sbjct: 420 VAIAKWLATDPKLLILDSPTVGVDVGARAGIFDIVAKLAESGLAIILISDEVPEVYFNAD 479

Query: 483 RILMMKKGHVSAEY--RADELSEAD 505
           R+L M +G +   Y  R   L E +
Sbjct: 480 RVLHMAQGRIVGTYDPRQSRLEEIE 504



 Score = 69.7 bits (169), Expect = 2e-16
 Identities = 53/219 (24%), Positives = 106/219 (48%), Gaps = 7/219 (3%)

Query: 289 DVSFKLHGGEILGVTGLLDSGRNELARALAGV-APAQSGDVLLDGQQIALRTPSDAKRHR 347
           +VSF++  GE+  + G    G++ L + + GV  PA+   +  DG+     +P  A+   
Sbjct: 37  NVSFEVQPGEVHCLAGENGCGKSTLIKVITGVYRPAEGAVIEYDGETYPHMSPVTAQDRG 96

Query: 348 IGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPG 407
           I  + +D     LF +  + +N+    +   R R   +D  R + +A   +  L I T  
Sbjct: 97  IQVIWQDL---ALFPEMTVAENIAFHEVLGGRPRL--VDYGRMRRIAVDALGRLGI-TLD 150

Query: 408 VDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGI 467
           VD P++  +   +Q V I R L  + +++ +  PT  +     D +  I++ LS  G+ +
Sbjct: 151 VDLPLKEYAIAQRQIVAIARALVGEAKLVFMDEPTASLTQSETDHLLEIVRSLSASGVAV 210

Query: 468 ILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADL 506
           + +S  L E+L+   RI +++ G +   Y A  ++++ +
Sbjct: 211 VFVSHRLAEVLEISSRITVLRDGALVGVYPAAGMTQSKI 249


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: 620
Number of extensions: 31
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: 509
Length adjustment: 35
Effective length of query: 480
Effective length of database: 474
Effective search space:   227520
Effective search space used:   227520
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