GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcF in Bacillus altitudinis 41KF2b

Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate WP_035704441.1 BA79_RS18275 (Fe-S)-binding protein

Query= reanno::Smeli:SMc00926
         (443 letters)



>NCBI__GCF_000691145.1:WP_035704441.1
          Length = 446

 Score =  228 bits (582), Expect = 2e-64
 Identities = 146/423 (34%), Positives = 212/423 (50%), Gaps = 31/423 (7%)

Query: 32  ETILRKCVHCGFCTATCPTYVVLGD-ELDSPRGRIYLIKDMLENGRAADSETVTHIDRCL 90
           E  L  C+ CGFC  +CPTY+  G  E  SPRGRI L+K + +     D +    ++ CL
Sbjct: 20  EKELLNCMRCGFCLPSCPTYIESGQQETHSPRGRIALMKAVRDGVIEPDEDVEHSLNLCL 79

Query: 91  SCLSCLTTCPSGVDYMHLVDHARAHIEKTYKRPFKDRLARSVIAATLPYPSRFRLALGAA 150
            C +C   CPSGV Y  L++ AR  I++  K+ F  +L R V+   L +PS+ R+   A+
Sbjct: 80  GCRACEPVCPSGVKYGQLLEDARDIIQQHKKQSFPVKLMRRVVFKGL-FPSQSRMRQAAS 138

Query: 151 GL----ARPLAGLLKRVPFLRTLGVMLDLAPSALPAARGAKPA---VYAAKGTPRARVAL 203
            L       L    ++   L+ L   L L   ALP     K      Y A G  + RVA 
Sbjct: 139 FLRFYQTSGLQTAARKTRILKVLPSHLQLMEQALPKVPPQKKKRLNEYKAIGQAKKRVAF 198

Query: 204 LTGCAQPVLRPEINDATIRLLTGQGVEVVVSAGEGCCGALVHHMGRDEQALQAGRHNIDV 263
            TGC    +    N ATI LL   G +V+V   + CCGAL  H G  +QA Q  + NI+ 
Sbjct: 199 FTGCLMDTVFSNTNKATIHLLQLAGCDVIVPPIQTCCGALHGHSGEKDQAKQLAKRNIE- 257

Query: 264 WLKAAEEDGLDAIIITASGCGTTIKDYGHMLRLDPAYAEKAARVSALAKDVTEYLATLD- 322
              A EE   DAII+ A GCG  + DYGH+L+ DP + +++   S    D++  L  L+ 
Sbjct: 258 ---AFEETDADAIIMNAGGCGAFLSDYGHLLQDDPDFQKRSKAFSQKITDISSILVELEF 314

Query: 323 -------LPEQGARNLTVAYHSACSMQHGQKITSAPKQLLKR-AGFSVREPAEGHLCCGS 374
                  LP Q      + Y  +C +++G  +  AP+ L+K   G + +E  +   CCGS
Sbjct: 315 HCRVPLALPAQ-----VITYQDSCHLRNGMNVQQAPRVLMKAIQGVTFKEMKDAGRCCGS 369

Query: 375 AGTYNILQPEISAKLKARKVRNIEATKPEVIATGNIGCITQIASGTE----IPILHTVEL 430
           AG YNILQP++S ++   K+     T    I T N GC  Q+A+G +    +P +  + L
Sbjct: 370 AGIYNILQPDMSMQILDHKMTEASNTAAAAIVTSNPGCQLQMAAGVKKAGHMPSMRAIHL 429

Query: 431 LDW 433
            D+
Sbjct: 430 ADF 432


Lambda     K      H
   0.320    0.135    0.409 

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: 450
Number of extensions: 28
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 443
Length of database: 446
Length adjustment: 32
Effective length of query: 411
Effective length of database: 414
Effective search space:   170154
Effective search space used:   170154
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: 51 (24.3 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:

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:

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