GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_11890 in Sinorhizobium meliloti 1021

Align Inositol transport system ATP-binding protein (characterized)
to candidate SM_b21376 SM_b21376 sugar uptake ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>lcl|FitnessBrowser__Smeli:SM_b21376 SM_b21376 sugar uptake ABC
           transporter ATP-binding protein
          Length = 503

 Score =  421 bits (1083), Expect = e-122
 Identities = 230/497 (46%), Positives = 330/497 (66%), Gaps = 12/497 (2%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           +L+I +++K F  V AL  ++L VR G V  L+GENGAGKSTLMKI+AG++   +GEI L
Sbjct: 9   ILKITDVTKSFGQVAALKGMRLEVRRGRVHTLLGENGAGKSTLMKILAGVHGATSGEIVL 68

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142
            G+      P  A   G+A++ QEL+L  ++++AENI   RE       +N + +     
Sbjct: 69  DGQAYRPANPQEAASLGLAIVFQELSLCNNLTVAENILATREP-RRFGFINDKALVAKAH 127

Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202
            ++A LR+ +D  E+VGNLSIA+RQ+VEIAK +S+D+ ++I+DEPTS++++ E   LF I
Sbjct: 128 RIVADLRLPIDVTEKVGNLSIAQRQLVEIAKGLSHDAKVVILDEPTSSLSDSEAEILFEI 187

Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262
           I  L+ +G  I+YI+H+M E+  ++D++ V RDG Y+     D +  ++LI++MVGR + 
Sbjct: 188 IGRLRQRGAAIIYISHRMEEIMRLSDDITVIRDGEYVSTHARDEVTIETLIALMVGRRMD 247

Query: 263 QLFPLRETPIGDL------LLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAE 316
           +++P    P+  +      +L V  LT +G F+DVSFD+ AGEILG  GL+GSGR+ V  
Sbjct: 248 EIYP---PPVHHVAADRAPVLAVDRLTREGEFQDVSFDVRAGEILGFFGLVGSGRSEVMN 304

Query: 317 TIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL 376
            +FG+  S++G + LDG+ VR   P  AI +G   +TE+RK  GL    SV  N+ MA L
Sbjct: 305 ALFGMK-SAAGTVRLDGEVVRFRSPDQAIARGVGFVTENRKEEGLVLGHSVEWNISMAAL 363

Query: 377 PHYTGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRL 435
             + G  GFI+  A RA   +   KL +KT SLE     LSGGNQQK +LA+WL+T P++
Sbjct: 364 ADFAGGLGFIRNGAERAAASEQVGKLSIKTNSLETPAGALSGGNQQKIVLAKWLLTRPKV 423

Query: 436 LILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGT 495
           LILDEPTRG+DVGAK EIY++I  LA+EG A+++ISS+LPEVLGMSDRV+VMHEG    T
Sbjct: 424 LILDEPTRGVDVGAKFEIYKIIRELAAEGTAILLISSDLPEVLGMSDRVVVMHEGAPGAT 483

Query: 496 LDRSEATQEKVMQLASG 512
           L+ S  T E +M  A+G
Sbjct: 484 LEGSALTPETIMAHATG 500


Lambda     K      H
   0.320    0.136    0.381 

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: 592
Number of extensions: 29
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 517
Length of database: 503
Length adjustment: 34
Effective length of query: 483
Effective length of database: 469
Effective search space:   226527
Effective search space used:   226527
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.

Links

Downloads

Related tools

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