Alignments for a candidate for PS417_11890 in Clostridium tyrobutyricum FAM22553

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Clostridium tyrobutyricum FAM22553

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_039653025.1 PN53_RS09475 ABC transporter ATP-binding protein

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



>NCBI__GCF_000816635.1:WP_039653025.1
          Length = 512

 Score =  299 bits (765), Expect = 2e-85
 Identities = 170/496 (34%), Positives = 281/496 (56%), Gaps = 15/496 (3%)

Query: 18  LEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA 77
           + + Y L + NI+K F  VVA  ++   V+ G + AL+GENGAGKSTLM +++GIY PD 
Sbjct: 1   MNKEYYLSMKNITKKFGDVVANNNINFNVKGGEIHALLGENGAGKSTLMNMLSGIYIPDG 60

Query: 78  GEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREM 137
           G I + G+   F++P  A K+G+ MI+Q   L+  M+  +NI +G ++   L   N+ + 
Sbjct: 61  GSIFIHGREARFKSPTDAIKSGVGMIYQHFKLIESMTAIQNILLGNKRKIFL---NYDQE 117

Query: 138 HRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVA 197
            +   ++  +   ++D  + V ++S+ ER+ +EI K +   +DILI+DEPT+  T +E  
Sbjct: 118 LKKIQKIQDKYGFDVDLNKYVYDMSVGERENLEILKVLCRGADILILDEPTAVFTPQETK 177

Query: 198 HLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMV 257
            LF ++  +K +G  I++ITHK++EV  +AD + + R G  +   + +      L+  M+
Sbjct: 178 KLFDLMNRMKKEGCSIIFITHKLDEVMEVADSITILRKGESVETVKKEDTTPKELVDKMI 237

Query: 258 GRELSQLFPLRETPIGDLLLTVRDLTLDG-----VFKDVSFDLHAGEILGIAGLMGSGRT 312
           G  +        T IG  +L V DL L       V K+++F++H GE++GIAG+ G G+ 
Sbjct: 238 GYHVDLAIKRSNTTIGKTILKVSDLNLINDANIPVLKNINFEIHEGEVVGIAGISGCGQK 297

Query: 313 NVAETIFGITPSSSGQITLDGKAVRISDPHMAIEK--GFALLTEDRKLSGLFPCLSVLEN 370
            + E I G+T  SSG+I  +GK +   D     ++  G + + EDR   GL   + +++N
Sbjct: 298 ELCEAIAGVTKISSGKIEFEGKDITCKDSAKLAKENIGISFVPEDRIGMGLVGSMDMVDN 357

Query: 371 MEMAVLPHYT-GNGFIQQK-ALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARW 428
           +   +L HY    G+I +K  +    + +   L VKTP++   I  LSGGN QK LL R 
Sbjct: 358 V---LLKHYKYQKGYILKKDDMEKESQKIKDDLDVKTPNIHYPIKNLSGGNIQKILLGRE 414

Query: 429 LMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMH 488
           L  NP+LL++  P RG+D+     IY L+     +G  V+ +  +L  +L + DR++VMH
Sbjct: 415 LGLNPKLLLMGYPVRGLDINTCYTIYNLVNKEKEKGTGVLFVGEDLDILLNLCDRIIVMH 474

Query: 489 EGELMGTLDRSEATQE 504
            GE+ G  +  +AT+E
Sbjct: 475 SGEITGNFESEKATKE 490



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 49/228 (21%), Positives = 112/228 (49%), Gaps = 18/228 (7%)

Query: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349
           +++F++  GEI  + G  G+G++ +   + GI     G I + G+  R   P  AI+ G 
Sbjct: 24  NINFNVKGGEIHALLGENGAGKSTLMNMLSGIYIPDGGSIFIHGREARFKSPTDAIKSGV 83

Query: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTP--- 406
            ++ +  KL      ++ ++N+ +       GN   ++K      +++ K  +++     
Sbjct: 84  GMIYQHFKL---IESMTAIQNILL-------GN---KRKIFLNYDQELKKIQKIQDKYGF 130

Query: 407 --SLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEG 464
              L + +  +S G ++   + + L     +LILDEPT         +++ L+  +  EG
Sbjct: 131 DVDLNKYVYDMSVGERENLEILKVLCRGADILILDEPTAVFTPQETKKLFDLMNRMKKEG 190

Query: 465 MAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512
            ++I I+ +L EV+ ++D + ++ +GE + T+ + + T ++++    G
Sbjct: 191 CSIIFITHKLDEVMEVADSITILRKGESVETVKKEDTTPKELVDKMIG 238



 Score = 63.9 bits (154), Expect = 1e-14
 Identities = 40/229 (17%), Positives = 105/229 (45%), Gaps = 6/229 (2%)

Query: 36  VVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFE--TPL 93
           +  L ++   +  G V+ + G +G G+  L + IAG+ +  +G+I   GK I  +    L
Sbjct: 270 IPVLKNINFEIHEGEVVGIAGISGCGQKELCEAIAGVTKISSGKIEFEGKDITCKDSAKL 329

Query: 94  AAQKAGIAMIHQE---LNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAELLARLRI 150
           A +  GI+ + ++   + L+  M + +N+ +   +    +++   +M + + ++   L +
Sbjct: 330 AKENIGISFVPEDRIGMGLVGSMDMVDNVLLKHYKYQKGYILKKDDMEKESQKIKDDLDV 389

Query: 151 NL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQ 209
              +    + NLS    Q + + + +  +  +L+M  P   +       +++++   K +
Sbjct: 390 KTPNIHYPIKNLSGGNIQKILLGRELGLNPKLLLMGYPVRGLDINTCYTIYNLVNKEKEK 449

Query: 210 GKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVG 258
           G G++++   ++ +  + D + V   G   G   ++    + +   M+G
Sbjct: 450 GTGVLFVGEDLDILLNLCDRIIVMHSGEITGNFESEKATKEIIGYKMLG 498


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: 538
Number of extensions: 30
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 517
Length of database: 512
Length adjustment: 35
Effective length of query: 482
Effective length of database: 477
Effective search space:   229914
Effective search space used:   229914
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources