Alignments for a candidate for ytfR in Nitriliruptor alkaliphilus DSM 45188

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Nitriliruptor alkaliphilus DSM 45188

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_052665037.1 NITAL_RS04930 sugar ABC transporter ATP-binding protein

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



>NCBI__GCF_000969705.1:WP_052665037.1
          Length = 511

 Score =  320 bits (819), Expect = 1e-91
 Identities = 191/503 (37%), Positives = 291/503 (57%), Gaps = 22/503 (4%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADR--GTI 66
           IL    ++K FPGVKAL++V+ ++ RGEI A+ GENGAGKSTL+  L+GVY A    G I
Sbjct: 4   ILEMREITKTFPGVKALEDVNLTVARGEIHAICGENGAGKSTLMNVLSGVYPAGTYTGEI 63

Query: 67  WLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRA 126
             +G+ +  ++   ++ LGI  ++QE+ L+P++SVA+N+F+G E  R G++   E  + A
Sbjct: 64  VFDGEPVEHQSINDSEALGIVIIHQELALIPHLSVAENIFLGNEQSRRGVIDWHETNRMA 123

Query: 127 TELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186
            EL+   G   +   P+ +  V  QQ++ I +A+    K+LILDEPTA+L+ Q+   L  
Sbjct: 124 GELLQRVGLDENPTTPVGQLGVGKQQLIEIAKALSKDVKLLILDEPTAALNDQDSAHLLG 183

Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELP-----QIELVKMM 241
           L+RQLR  G++ I ++H L+++ +++D  T++R+G  +   ET ++      Q  +++ M
Sbjct: 184 LLRQLRAEGITCIMISHKLNELLEIADATTIIRDGRTI---ETLDMSDPDSNQRRMIRGM 240

Query: 242 LGRELDTHALQRAG----RTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGS 297
           +GR++D+   +R           +           +  +   +L VR GEIVG+AGL+G+
Sbjct: 241 VGRDIDSLYPERQATLGEEVFRVEDWTVMHPTQAGRVIVEGANLSVRAGEIVGIAGLMGA 300

Query: 298 GRTETAEVIFGIKPAD--SGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASV 355
           GRTE A  IFG       SG   + G+  +  +   A   GI +  EDRK  G+     +
Sbjct: 301 GRTELAMSIFGRTYGRDVSGQVYMHGQQVDTHTVDAAISHGIAYATEDRKRYGLNLIEDI 360

Query: 356 RENI---ILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVL 412
           R NI    L   +  GW   +   ++  +AER+ R L IR PS    +  LSGGNQQKV+
Sbjct: 361 RRNISASALGKLSHNGW---VDGNQEIAVAERYRRDLDIRAPSVMSVVGKLSGGNQQKVV 417

Query: 413 LSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRV 472
           LS+WL T P+ LILDEPTRGIDVGA  EI  ++  L   G A+LVISSEL EL+G  DR+
Sbjct: 418 LSKWLYTDPELLILDEPTRGIDVGAKFEIYTIVNRLAEAGKAVLVISSELPELLGICDRI 477

Query: 473 IIMRDRKQVAEIPLAELSVPAIM 495
             +   +   E+P AE +   +M
Sbjct: 478 YTLSAGRITGELPAAEATQERLM 500



 Score = 66.2 bits (160), Expect = 3e-15
 Identities = 57/247 (23%), Positives = 110/247 (44%), Gaps = 13/247 (5%)

Query: 7   QEILRTEGLSKFFP---GVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTG-VYHAD 62
           +E+ R E  +   P   G   ++  + S+R GEI+ + G  GAG++ L  ++ G  Y  D
Sbjct: 258 EEVFRVEDWTVMHPTQAGRVIVEGANLSVRAGEIVGIAGLMGAGRTELAMSIFGRTYGRD 317

Query: 63  -RGTIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKE 121
             G +++ GQ +       A   GI    ++      +++ +++         G L    
Sbjct: 318 VSGQVYMHGQQVDTHTVDAAISHGIAYATEDRKRY-GLNLIEDIRRNISASALGKLSHNG 376

Query: 122 MEKRATELMAS--YGFSLDVREP-----LNRFSVAMQQIVAICRAIDLSAKVLILDEPTA 174
                 E+  +  Y   LD+R P     + + S   QQ V + + +    ++LILDEPT 
Sbjct: 377 WVDGNQEIAVAERYRRDLDIRAPSVMSVVGKLSGGNQQKVVLSKWLYTDPELLILDEPTR 436

Query: 175 SLDTQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQ 234
            +D      ++ ++ +L + G +++ ++  L ++  + DRI  L  G   G     E  Q
Sbjct: 437 GIDVGAKFEIYTIVNRLAEAGKAVLVISSELPELLGICDRIYTLSAGRITGELPAAEATQ 496

Query: 235 IELVKMM 241
             L+++M
Sbjct: 497 ERLMELM 503


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: 585
Number of extensions: 37
Number of successful extensions: 9
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: 500
Length of database: 511
Length adjustment: 34
Effective length of query: 466
Effective length of database: 477
Effective search space:   222282
Effective search space used:   222282
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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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