GapMind for catabolism of small carbon sources

 

Aligments 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_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>lcl|FitnessBrowser__Smeli:SM_b20673 SM_b20673 sugar uptake ABC
           transporter ATP-binding protein
          Length = 526

 Score =  380 bits (976), Expect = e-110
 Identities = 212/505 (41%), Positives = 322/505 (63%), Gaps = 14/505 (2%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L  + I K F GV AL  V F++  G++H LMGENGAGKSTL+K+L G Y    G V +D
Sbjct: 19  LAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYEGAVRVD 78

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLG-WVNKREAKRFVRE 123
           G  VRF++   + AAGIA+IHQEL  VP+L VA+N+ LG+     G +V+++ +    R 
Sbjct: 79  GETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVDRKASLEAARG 138

Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183
            L  +G+ LDP A++ +L + ++Q+VEI KAL   AR++ +DEPTS+LS  E   LFK++
Sbjct: 139 LLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGECRRLFKIM 198

Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243
           R L AD   +IYISHR+DE+ +L D  T+FRDGR + + P + G+  +TI++ MVGR + 
Sbjct: 199 RQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARP-MAGLDENTIIAAMVGRNLL 257

Query: 244 DIYNY-----SARPLGEVRFAAKGIEG----HALAQPASFEVRRGEIVGFFGLVGAGRSE 294
           D +          P+  VR  +  + G      + +  SF+VR GEI+G  GL+GAGR+E
Sbjct: 258 DAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGAGRTE 317

Query: 295 LMHLVYGADH-KKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENIN 353
           ++  ++ ++   +GGE+ LDG  + +RS  +A R G  L  EDRK +G+    ++ +N+ 
Sbjct: 318 ILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESIRDNVA 377

Query: 354 ISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAE 413
           +       R G+    + E   A   +  L ++     Q    LSGGNQQK ++ +WLA 
Sbjct: 378 LPLVGRLARFGL-RSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVIGKWLAT 436

Query: 414 PDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQG 473
              +V++LDEPTRGIDVGAK EIY++I++LA  G AIV++SSELPE+L ++DRI+VM +G
Sbjct: 437 GP-RVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVMAEG 495

Query: 474 RISGELTRKDATEQSVLSLALPQSS 498
           R +G ++R++A+E+ ++ LA P+S+
Sbjct: 496 RQTGLISREEASEERIMQLAAPRSA 520



 Score = 98.6 bits (244), Expect = 5e-25
 Identities = 71/249 (28%), Positives = 122/249 (48%), Gaps = 19/249 (7%)

Query: 226 EGVTRDTIVSEMVGREISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFF 285
           + + RD++ +E            S RP+      +K   G A  +   FE+R GEI    
Sbjct: 3   DAIPRDSVTTE------------SDRPILAAEAISKSFGGVAALKDVRFELRAGEIHALM 50

Query: 286 GLVGAGRSELMHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAM 345
           G  GAG+S LM ++ G      G + +DG+ ++  +  +A   GI +     +E  +V  
Sbjct: 51  GENGAGKSTLMKVLSGVYTDYEGAVRVDGETVRFSNVRDAEAAGIAII---HQELNLVPE 107

Query: 346 ATVSENINISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKA 405
             V++NI +   R  +  G+F+DRK   E A   +  L I+      ++  L  G QQ  
Sbjct: 108 LGVADNIFLG--RERVIAGLFVDRKASLEAARGLLNRLGIEL-DPEARVGQLRVGEQQLV 164

Query: 406 ILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSD 465
            +++ L+  + +++I+DEPT  +  G    ++ ++ QLA  G  I+ IS  + EV+ +SD
Sbjct: 165 EIAKALS-VEARILIMDEPTSALSPGECRRLFKIMRQLAADGVGIIYISHRIDEVMQLSD 223

Query: 466 RIVVMRQGR 474
           R+ V R GR
Sbjct: 224 RVTVFRDGR 232


Lambda     K      H
   0.320    0.136    0.385 

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: 723
Number of extensions: 50
Number of successful extensions: 13
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: 512
Length of database: 526
Length adjustment: 35
Effective length of query: 477
Effective length of database: 491
Effective search space:   234207
Effective search space used:   234207
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:

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. 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:

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, 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