GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Phaeobacter inhibens BS107

Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC

Query= uniprot:Q31RN9
         (396 letters)



>FitnessBrowser__Phaeo:GFF196
          Length = 432

 Score =  213 bits (543), Expect = 7e-60
 Identities = 145/415 (34%), Positives = 223/415 (53%), Gaps = 58/415 (13%)

Query: 17  WLRQNLFSSWLNSAITLLLVVIIVTVVGRL------GLWITTE-------------ARWT 57
           W+R+NLFSS  NS +TL  + +I  ++         G+W T               A ++
Sbjct: 32  WIRENLFSSVPNSILTLAALALIYALLSSTLPWLLNGVWTTNSLAECREVLDGKLGACFS 91

Query: 58  VLVDNWTLFFVG-RYPAAEQWR----LWLWLGLLSPTLG-------LTWGCLATGSHRWQ 105
           VL + W     G +YP  E WR    L L L  L+P L        L +  +      W 
Sbjct: 92  VLTERWNQLLYGFKYPGTEYWRPNLALVLLLVALAPVLFFDLPRKLLAFTAIYPFLAFWL 151

Query: 106 RRSLWGWAGLAAAIAGIPLPWFPHKLGLAAIAATVPAASWLAQRC-RGQAWLRFLPTLWG 164
              +WG + L   +A          LG  A       A ++ Q+  +G   L F   +  
Sbjct: 152 ---IWGGSILVPIVA---------LLGFVA-------AGFVFQKFGKGSFALGFFGAIVA 192

Query: 165 --VLFLVGLWLLQGGLG----LRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQS 218
             V++ +G +L+  G      L  V S D  G +L +   +  +  S+PLGI LALGRQS
Sbjct: 193 AVVVWNIGGFLIPEGASDNAMLSAVPSRDLGGFMLNMMLGVTCVSLSVPLGIALALGRQS 252

Query: 219 SLPAIRWLSVTYIELFRGLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYL 278
           ++P I+W+ V +IE  RG+PL+T+LF   VM+      +  +D  LR ++ +T+F +AY+
Sbjct: 253 NMPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPPDATVDLFLRVVIMITLFSAAYI 312

Query: 279 AETVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLL 338
           AE +RGGL A+P+GQ+EAA +LGL+  Q  R I+LPQAL+ISIP IV + + L +DTTL+
Sbjct: 313 AEVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQALKISIPGIVNVAVGLFKDTTLV 372

Query: 339 SIVGLLELLGISRS-ILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392
           S++ + +L+G+ R  ILA+  + G Y E+  F   L+++ CYG++Q S+ LE+RL
Sbjct: 373 SVISMFDLVGMIRGPILASTEWNGVYWELLGFAAFLFFIVCYGISQYSQWLERRL 427


Lambda     K      H
   0.329    0.142    0.471 

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: 452
Number of extensions: 17
Number of successful extensions: 4
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: 396
Length of database: 432
Length adjustment: 31
Effective length of query: 365
Effective length of database: 401
Effective search space:   146365
Effective search space used:   146365
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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