GapMind for catabolism of small carbon sources

 

Aligments 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)



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