GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natF in Methylocystis bryophila S285

Align NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_245299991.1 B1812_RS19680 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q8YPM9
         (369 letters)



>NCBI__GCF_002117405.1:WP_245299991.1
          Length = 350

 Score =  255 bits (652), Expect = 1e-72
 Identities = 134/356 (37%), Positives = 196/356 (55%), Gaps = 11/356 (3%)

Query: 18  KLAVILGASLIFTTTACGGDSAPTTDTSTNSGSTLVANRWNTIKNRGQLICGVSGEVPGF 77
           K A++L   + F   A  G         + + STL       I+ RG ++CG +   PGF
Sbjct: 2   KFAILLFLLMAFGLVA--GAPRLAAQPESKASSTL-----QEIRRRGVVVCGATAPAPGF 54

Query: 78  SFVGTDGEYSGIDVDVCRAIAAALFDNPDAVEFRNLSAKERFTALQTGEVDILSRNTTWT 137
           + +   G +SG D+D CRA+A A  D+P  +    L  K+R  AL +G+VD+L     WT
Sbjct: 55  AVMDEAGSWSGFDIDFCRALAVAALDDPQKIRIETLQQKQRLPALHSGDVDVLLSGAPWT 114

Query: 138 LSRATSVGLEFAPVVFYDGQAIMVRKNSAIKSL----ADLKDKAICVQTGTTTEQNLADQ 193
            +R     L +  + FY GQ  + R+           A      +CVQ G ++E NLA  
Sbjct: 115 EAREAGHQLLYGAISFYGGQGFLGRRAWGPTGEPWRGAGGTPPRVCVQQGGSSELNLAQF 174

Query: 194 MRKRNITYKPVVFEDVNVTFATYAEGRCDAITADRSALVSRRTTLPTPEDNVVLDEVISS 253
            R+  + Y+PV F  +      Y  G CD  +AD   L   R+ L  P+D+VV   +IS 
Sbjct: 175 YREHGVAYRPVAFGSLEEAARAYDAGDCDLFSADLVELHQWRSRLQKPDDHVVAPALISK 234

Query: 254 EPLAPAVARGDAKWSNTVNWVVYALIKGEELGINAQNLGQFTTSNDPDVKRFLGTEGDLG 313
            PL P V +GD +W N V W ++A++  EELG++A+ +    +S+ PD++R +G++GD G
Sbjct: 235 SPLGPIVRQGDDQWFNVVRWTLFAMVDAEELGVDAKTVDAALSSDIPDLRRLVGSDGDFG 294

Query: 314 QGLGLTNDFAARIIKHVGNYAEVYDRNLGPKTKLNLARGQNQLWSKGGLLYSPPFR 369
           +GLGL  D+A R+I  VGNYAEV+DRNLG  +   + R QN LWSKGGL+Y+PP R
Sbjct: 295 EGLGLRPDWAYRVIHEVGNYAEVFDRNLGKSSPFAMERRQNALWSKGGLMYAPPVR 350


Lambda     K      H
   0.317    0.133    0.387 

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: 340
Number of extensions: 16
Number of successful extensions: 2
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: 369
Length of database: 350
Length adjustment: 29
Effective length of query: 340
Effective length of database: 321
Effective search space:   109140
Effective search space used:   109140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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:

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