Alignments for a candidate for ytfR in Stutzerimonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Stutzerimonas stutzeri A1501

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_041755622.1 PST_RS14570 ABC transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>NCBI__GCF_000013785.1:WP_041755622.1
          Length = 518

 Score =  256 bits (654), Expect = 1e-72
 Identities = 165/472 (34%), Positives = 257/472 (54%), Gaps = 11/472 (2%)

Query: 14  GLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAI 73
           G++K +PG  A D +D S++ GEI ALLGENGAGKSTL+K + GV   D G I  +G+ +
Sbjct: 13  GITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGAIHWQGERV 72

Query: 74  SPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATELMASY 133
           + ++ A A++ GIG V+Q  +L   +SVA+N+ +    K       K++E +  E+   Y
Sbjct: 73  TMRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAG---TPKQLEPKIREVSQRY 129

Query: 134 GFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRD 193
           G  L+ +  ++  S+  +Q V I R +    ++LILDEPT+ L  QE + LF  +R+L  
Sbjct: 130 GMPLEPQRLVHSLSIGERQRVEIVRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAA 189

Query: 194 RGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG--RELDTHAL 251
            G S++F++H L++V  +    TVLR G   G     E   +EL ++M+G    L+    
Sbjct: 190 EGCSILFISHKLNEVRALCQSATVLRGGRVSGECIPAECSDLELARLMVGDAEGLEAEYP 249

Query: 252 QRAGRTLLSDKPVAAFKNYGKKG-TIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIK 310
           +  GR         ++ N    G ++   DLEVR GEIVG+AG+ G+G+ E   ++ G +
Sbjct: 250 KSEGRAPFLRVERLSWHNADPFGVSLEEVDLEVRAGEIVGIAGVAGNGQDELLALLSGEQ 309

Query: 311 PADSGTAL---IKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367
              +  A+     G       P      G+ F P +R   G + + S+ +N +L    Q 
Sbjct: 310 RLPAAQAMRIRFLGDDVAHLRPDARRRHGMAFVPAERLGHGAVPSMSLADNGLLTAFQQT 369

Query: 368 GWLRP--ISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLI 425
           G +    I R + +  AE+ I++  ++TP  + P   LSGGN QK +L R +L +P+ LI
Sbjct: 370 GMVERGLIRRGKVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGREILQQPKLLI 429

Query: 426 LDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRD 477
              PT G+DVGA A I R +  L   G A+LVIS +LEEL   +DR+  + D
Sbjct: 430 AAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAALSD 481



 Score = 87.0 bits (214), Expect = 1e-21
 Identities = 64/211 (30%), Positives = 106/211 (50%), Gaps = 9/211 (4%)

Query: 280 DLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGF 339
           DL ++PGEI  L G  G+G++   ++I+G+   D+G    +G+   +R P QA   GIG 
Sbjct: 28  DLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGAIHWQGERVTMRDPAQARERGIGM 87

Query: 340 CPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQP 399
             +      +    SV ENI LAL A+ G  + +  K + E+++R+   L       ++ 
Sbjct: 88  VFQHFS---LFETLSVAENIALALGAKAGTPKQLEPKIR-EVSQRYGMPL-----EPQRL 138

Query: 400 IEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVIS 459
           +  LS G +Q+V + R L+   + LILDEPT  +      E+   +  L A+G ++L IS
Sbjct: 139 VHSLSIGERQRVEIVRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSILFIS 198

Query: 460 SELEELVGYADRVIIMRDRKQVAEIPLAELS 490
            +L E+        ++R  +   E   AE S
Sbjct: 199 HKLNEVRALCQSATVLRGGRVSGECIPAECS 229



 Score = 72.0 bits (175), Expect = 5e-17
 Identities = 70/260 (26%), Positives = 111/260 (42%), Gaps = 37/260 (14%)

Query: 10  LRTEGLS--KFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTG---------- 57
           LR E LS     P   +L+ VD  +R GEI+ + G  G G+  L+  L+G          
Sbjct: 258 LRVERLSWHNADPFGVSLEEVDLEVRAGEIVGIAGVAGNGQDELLALLSGEQRLPAAQAM 317

Query: 58  --------VYHADRGTIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADN----L 105
                   V H         G A  P     A++LG G V       P+MS+ADN     
Sbjct: 318 RIRFLGDDVAHLRPDARRRHGMAFVP-----AERLGHGAV-------PSMSLADNGLLTA 365

Query: 106 FIGREPKRFGLLRRKEMEKRATELMASYGFSL-DVREPLNRFSVAMQQIVAICRAIDLSA 164
           F        GL+RR ++   A +++  +     D + P    S    Q   + R I    
Sbjct: 366 FQQTGMVERGLIRRGKVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGREILQQP 425

Query: 165 KVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFV 224
           K+LI   PT  +D      +   + +LRD G +++ ++  L++++Q+SDRI  L +G   
Sbjct: 426 KLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAALSDGRLS 485

Query: 225 GCRETCELPQIELVKMMLGR 244
             R T     +E+ + M G+
Sbjct: 486 PQRATASTCPVEVGRWMAGQ 505


Lambda     K      H
   0.321    0.138    0.391 

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: 560
Number of extensions: 29
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 500
Length of database: 518
Length adjustment: 34
Effective length of query: 466
Effective length of database: 484
Effective search space:   225544
Effective search space used:   225544
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.

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

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