Alignments for a candidate for ytfR in Collimonas arenae Ter10

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Collimonas arenae Ter10

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_061533691.1 CAter10_RS12710 sugar ABC transporter ATP-binding protein

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



>NCBI__GCF_001584165.1:WP_061533691.1
          Length = 516

 Score =  484 bits (1246), Expect = e-141
 Identities = 258/493 (52%), Positives = 336/493 (68%), Gaps = 3/493 (0%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69
           L   G+ K F GVKAL +V   L  GE+  L+G+NGAGKSTLIK LTGV+  + GTI L 
Sbjct: 20  LELNGIYKAFGGVKALSDVSLRLYPGEVHTLMGQNGAGKSTLIKVLTGVHIPEHGTIRLN 79

Query: 70  GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATEL 129
           G+ + P +T  AQ LGI TVYQEVNL PN+SVA+N+FIGR P +FG +  K M+++A  L
Sbjct: 80  GREVRPTSTLEAQHLGISTVYQEVNLCPNLSVAENIFIGRYPTKFGAIDWKTMQRQAQRL 139

Query: 130 MASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189
           +      +DV  PL+R+ +A+QQ+VAI RA+ +SAKVLILDEPT+SLD  EV+LLF ++R
Sbjct: 140 LGDLQIDIDVTAPLSRYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQLLFSVLR 199

Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDTH 249
           +LR++G++++FVTHFL+Q Y +SDRITVLRNG   G     EL ++ELV  M+G ++ + 
Sbjct: 200 KLREQGMAILFVTHFLEQTYDISDRITVLRNGVLEGEYRVDELTRLELVNKMVGSQMQSE 259

Query: 250 ALQRAGRTLLSDKP--VAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307
                  T L D    V   +  G+KG +AP DL++R GE+ GL GLLGSGRTETA ++F
Sbjct: 260 VQAPDAATGLRDNAEIVLQARGLGRKGILAPLDLDLRAGEVYGLCGLLGSGRTETARLLF 319

Query: 308 GIKPADSGTALIKGKP-QNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQ 366
           G   ADSG   IK KP     SP +A   GIGFC EDRK +G I   SVRENIIL LQA+
Sbjct: 320 GADKADSGAISIKDKPLGKFGSPREAIAAGIGFCSEDRKQEGAILELSVRENIILGLQAR 379

Query: 367 RGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLIL 426
            G LR I RK QQ IA  +++ LGI+TP  E PI  LSGGNQQK LL+RWL T P  LIL
Sbjct: 380 AGLLRVIPRKRQQAIAADYVKWLGIKTPDIETPISSLSGGNQQKALLARWLATDPVILIL 439

Query: 427 DEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPL 486
           DEPTRGIDV A  EI+  +  LC  G+A+L ISSE+ E++  +DR++++RDR+   E   
Sbjct: 440 DEPTRGIDVRAKQEIMDHVIALCRKGMAILFISSEISEVLRCSDRMLVLRDREPCGEYLR 499

Query: 487 AELSVPAIMNAIA 499
            EL   +++  IA
Sbjct: 500 GELDDDSVLQVIA 512



 Score = 82.4 bits (202), Expect = 3e-20
 Identities = 68/238 (28%), Positives = 118/238 (49%), Gaps = 25/238 (10%)

Query: 4   DQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADR 63
           D  + +L+  GL +   G+ A   +D  LR GE+  L G  G+G++   + L G   AD 
Sbjct: 271 DNAEIVLQARGLGR--KGILA--PLDLDLRAGEVYGLCGLLGSGRTETARLLFGADKADS 326

Query: 64  GTIWLEGQAI----SPKNTAHAQQLGIGTVYQE---VNLLPNMSVADNLFIGREPKRFGL 116
           G I ++ + +    SP+    A   GIG   ++      +  +SV +N+ +G +  R GL
Sbjct: 327 GAISIKDKPLGKFGSPREAIAA---GIGFCSEDRKQEGAILELSVRENIILGLQA-RAGL 382

Query: 117 LR---RKEMEKRATELMASYGFSL-DVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEP 172
           LR   RK  +  A + +   G    D+  P++  S   QQ   + R +     +LILDEP
Sbjct: 383 LRVIPRKRQQAIAADYVKWLGIKTPDIETPISSLSGGNQQKALLARWLATDPVILILDEP 442

Query: 173 TASLDTQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETC 230
           T  +D +  + + D +  L  +G++++F++  + +V + SDR+ VLR+      RE C
Sbjct: 443 TRGIDVRAKQEIMDHVIALCRKGMAILFISSEISEVLRCSDRMLVLRD------REPC 494


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: 649
Number of extensions: 26
Number of successful extensions: 7
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: 516
Length adjustment: 34
Effective length of query: 466
Effective length of database: 482
Effective search space:   224612
Effective search space used:   224612
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 24 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:

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