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_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein

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



>lcl|FitnessBrowser__Smeli:SM_b20713 SM_b20713 sugar uptake ABC
           transporter ATP-binding protein
          Length = 513

 Score =  629 bits (1623), Expect = 0.0
 Identities = 318/491 (64%), Positives = 396/491 (80%), Gaps = 1/491 (0%)

Query: 22  YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81
           YLL    + K FPGVVAL DV+ +++ GTV ALMGENGAGKSTLMKI+AGIY PD GE++
Sbjct: 22  YLLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVK 81

Query: 82  LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141
           LRG  I  ++PL A + GIAMIHQELNLMP M++AENIWI RE  N    V+H EM R T
Sbjct: 82  LRGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMT 141

Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201
           A+L  RL+I+LDPE +V +LS+A RQMVEIAKAVSY+SD+LIMDEPTSA+TE+EVAHLF 
Sbjct: 142 AKLFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFE 201

Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261
           II DL+SQG GIVYITHKMNE+F IADE +VFRDG YIG   ++ +  D +I MMVGRE+
Sbjct: 202 IIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGREI 261

Query: 262 SQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGI 321
           +Q+FP  E PIGD++L+V++LTL+GVF+DVSFD+ AGEILG+AGL+GSGR+NVAET+FG+
Sbjct: 262 TQMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAETLFGV 321

Query: 322 TPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL-PHYT 380
           TP+SSG I +DGK V I   + AI    A LTEDRK +G    L +LENM++AVL   + 
Sbjct: 322 TPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVLQDKFV 381

Query: 381 GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDE 440
             GF+ ++ + A CE+M +KLRVKTP+L++ ++ LSGGNQQK L+ RWL+TNPR+LILDE
Sbjct: 382 KRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLLTNPRILILDE 441

Query: 441 PTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSE 500
           PTRGIDVGAKAEI+RL+  LA  G+AVIMISSE+PEVLGMSDR+MVMHEG + G LDR+E
Sbjct: 442 PTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGILDRAE 501

Query: 501 ATQEKVMQLAS 511
           ATQ KVM+LA+
Sbjct: 502 ATQIKVMELAA 512



 Score = 94.4 bits (233), Expect = 9e-24
 Identities = 62/241 (25%), Positives = 124/241 (51%), Gaps = 16/241 (6%)

Query: 282 LTLDGVFK---------DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLD 332
           LT +GV K         DV F L  G +  + G  G+G++ + + + GI     G++ L 
Sbjct: 24  LTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLR 83

Query: 333 GKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRA 392
           G  +R+  P  A+E G A++ ++  L    P ++V EN+ +   P     GF+    +R 
Sbjct: 84  GAGIRLKSPLDALENGIAMIHQELNL---MPFMTVAENIWIRREPK-NRFGFVDHGEMRR 139

Query: 393 LCEDMCKKLRVKT-PSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKA 451
           +   + ++L++   P +E  +  LS  N+Q   +A+ +     +LI+DEPT  +     A
Sbjct: 140 MTAKLFERLKIDLDPEIE--VRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVA 197

Query: 452 EIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLAS 511
            ++ +I  L S+G+ ++ I+ ++ E+  ++D   V  +G+ +GT   +E T++ ++++  
Sbjct: 198 HLFEIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMV 257

Query: 512 G 512
           G
Sbjct: 258 G 258


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: 688
Number of extensions: 27
Number of successful extensions: 5
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: 517
Length of database: 513
Length adjustment: 35
Effective length of query: 482
Effective length of database: 478
Effective search space:   230396
Effective search space used:   230396
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