Alignments for a candidate for BPHYT_RS16930 in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Sinorhizobium meliloti 1021

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate SM_b20855 SM_b20855 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:A0A165ZSX8
         (514 letters)



>FitnessBrowser__Smeli:SM_b20855
          Length = 504

 Score =  388 bits (997), Expect = e-112
 Identities = 216/485 (44%), Positives = 310/485 (63%), Gaps = 5/485 (1%)

Query: 21  IGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIGEQTMA 80
           I KSF G+ AL +++F   PG+VHAL+GENGAGKSTL+++LGG  IPS G++ I  +   
Sbjct: 11  ISKSFGGIHALRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPSQGEVVINGKRTE 70

Query: 81  FKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTLLKGLA 140
            +   D+ A G+ VIHQEL L P+++VAEN+FLG LP    L++R  LR++A  L+  L 
Sbjct: 71  LRDPRDARALGIVVIHQELALAPDLSVAENIFLGELPT---LISRFSLRRRAKQLIDRLG 127

Query: 141 DEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRDE 200
            +IDP   VG LS+  +Q+VEIAKALS+   +I FDEPT+ L A++  +L  II  LRD 
Sbjct: 128 FDIDPGRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDAMKLHQIIRGLRDR 187

Query: 201 GKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQDIYDYR 260
           G  ++Y+SHR++EVF I + +TV KDG  V T    +++  D ++  MVGR I +++  R
Sbjct: 188 GVGIVYISHRLDEVFDIADRMTVMKDGETVGTVAT-TDVKIDDIIRMMVGRPIANMFPER 246

Query: 261 P-RERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREG 319
             R  G   L VK L    +   VSF V  GEI+GL GL+G+GRTE+ R + G +    G
Sbjct: 247 SQRTIGAELLNVKKLNAGRMVRDVSFSVRAGEIVGLGGLIGSGRTEVARAIFGADPLDSG 306

Query: 320 SLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLR 379
           ++ L  K LKL+SPRDA+ AG+ L PEDRK+ G++    +  N  ++   S       L+
Sbjct: 307 TISLKGKALKLKSPRDAVKAGIGLVPEDRKEHGVVIDKPIRVNATMARMSSVVNALGFLK 366

Query: 380 GDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGID 439
              ER +     KSL++K  +    +  LSGGNQQK +L +W      V++LDEPTRG+D
Sbjct: 367 PALERTDVTALGKSLRLKASSIDAPVSSLSGGNQQKVVLAKWFHAGGDVIILDEPTRGVD 426

Query: 440 IGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNL 499
           +GAKAEIY +I+ LA DG AV+V+SS+  E+ G+ DR+L + +G +RGEL+    +E NL
Sbjct: 427 VGAKAEIYALINKLAEDGKAVLVISSEHQELFGLCDRVLAMGQGQIRGELTPSNYSEENL 486

Query: 500 LQLAL 504
           L L++
Sbjct: 487 LGLSM 491



 Score = 92.8 bits (229), Expect = 3e-23
 Identities = 66/231 (28%), Positives = 117/231 (50%), Gaps = 12/231 (5%)

Query: 278 GLH--EPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHDKELKLRSPRD 335
           G+H    V+F V  GE+  L G  GAG++ L+R+L G     +G +V++ K  +LR PRD
Sbjct: 17  GIHALRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPSQGEVVINGKRTELRDPRD 76

Query: 336 AIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSLK 395
           A A G+++  ++     + P  SV ENI +   P+  +   L R         KQ+    
Sbjct: 77  ARALGIVVIHQEL---ALAPDLSVAENIFLGELPTLISRFSLRR-------RAKQLIDRL 126

Query: 396 VKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAA 455
                 G+ +  LS  +QQ   + + LS  +K+++ DEPT  +      +++QII  L  
Sbjct: 127 GFDIDPGRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDAMKLHQIIRGLRD 186

Query: 456 DGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPR 506
            G+ ++ +S  L EV  I+DR+ V+ +G   G ++       +++++ + R
Sbjct: 187 RGVGIVYISHRLDEVFDIADRMTVMKDGETVGTVATTDVKIDDIIRMMVGR 237


Lambda     K      H
   0.320    0.138    0.391 

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: 691
Number of extensions: 33
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: 514
Length of database: 504
Length adjustment: 34
Effective length of query: 480
Effective length of database: 470
Effective search space:   225600
Effective search space used:   225600
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 (21.8 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