GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Sinorhizobium meliloti 1021

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Smeli:SM_b20673
          Length = 526

 Score =  437 bits (1125), Expect = e-127
 Identities = 247/513 (48%), Positives = 328/513 (63%), Gaps = 10/513 (1%)

Query: 13  AASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVY 72
           + ++ S  P++A   + K F GV AL + +FEL AGE+HALMGENGAGKSTLMK+LSGVY
Sbjct: 9   SVTTESDRPILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVY 68

Query: 73  QRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFI 132
               G + +DG+ V  +  R A+A GI IIHQELNL+  L  A NIF+GRE R   GLF+
Sbjct: 69  TDYEGAVRVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRE-RVIAGLFV 127

Query: 133 DEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192
           D       A  +  R+ +++DP   VG+L V  QQ+VEIAKALS ++R+LIMDEPT+AL+
Sbjct: 128 DRKASLEAARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALS 187

Query: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252
             E   LF+I+R L A GVGI+YISH++DE+ Q++DRV+V RDG+++   PM     +TI
Sbjct: 188 PGECRRLFKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTI 247

Query: 253 ISMMVGRALDGEQRIPPDTSRNDVVLEVRGLN---RGR-----AIRDVSFTLRKGEILGF 304
           I+ MVGR L    R        + VL VR L+    GR      ++ VSF +R GEILG 
Sbjct: 248 IAAMVGRNLLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGI 307

Query: 305 AGLMGAGRTEVARAIFGADP-LEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLA 363
            GL+GAGRTE+   IF ++  L  GEI + G    I+SP DA   G   ++EDRK  GL 
Sbjct: 308 GGLLGAGRTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLH 367

Query: 364 VGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQK 423
           +   ++ N+AL  +GR  R G       R  A+  V  L ++     Q A  LSGGNQQK
Sbjct: 368 LHESIRDNVALPLVGRLARFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQK 427

Query: 424 IVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSH 483
           +VI KWL     +L  DEPTRGIDVGAK EIY L+  LA  G AIV++SSELPE+L ++ 
Sbjct: 428 VVIGKWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLAD 487

Query: 484 RVLVMCEGRITGELARADATQEKIMQLATQRES 516
           R+LVM EGR TG ++R +A++E+IMQLA  R +
Sbjct: 488 RILVMAEGRQTGLISREEASEERIMQLAAPRSA 520



 Score = 92.8 bits (229), Expect = 3e-23
 Identities = 74/255 (29%), Positives = 123/255 (48%), Gaps = 15/255 (5%)

Query: 21  PVIALRNVCKRFPGVLA----LDNCQFELAAGEVHALMGENGAGKSTLMK-ILSGVYQRD 75
           PV+++R++     G       L    F++ AGE+  + G  GAG++ +++ I +      
Sbjct: 271 PVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGAGRTEILETIFASNEGLR 330

Query: 76  SGDILLDGKPVEITEPRQAQALGIGIIHQELN---LMNHLSAAQNI---FIGREPRKAMG 129
            G+I LDG  V I  PR A+ LG  ++ ++     L  H S   N+    +GR  R  + 
Sbjct: 331 GGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESIRDNVALPLVGRLARFGLR 390

Query: 130 LFIDEDELNRQAA-AIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPT 188
            F  E  L + A  A+  R           G L+   QQ V I K L+   RVL++DEPT
Sbjct: 391 SFEGERALAKGAVDALGVRCA---GTGQAAGTLSGGNQQKVVIGKWLATGPRVLLLDEPT 447

Query: 189 AALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETS 248
             ++     E++ +I  L   G+ IV +S ++ EL  +ADR+ VM +G+    +  +E S
Sbjct: 448 RGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVMAEGRQTGLISREEAS 507

Query: 249 MDTIISMMVGRALDG 263
            + I+ +   R+  G
Sbjct: 508 EERIMQLAAPRSARG 522


Lambda     K      H
   0.320    0.135    0.372 

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: 720
Number of extensions: 40
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: 520
Length of database: 526
Length adjustment: 35
Effective length of query: 485
Effective length of database: 491
Effective search space:   238135
Effective search space used:   238135
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:

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