GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Methanobacterium veterum MK4

Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_048081181.1 EJ01_RS06730 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_000745485.1:WP_048081181.1
          Length = 566

 Score =  109 bits (272), Expect = 1e-28
 Identities = 74/231 (32%), Positives = 119/231 (51%), Gaps = 8/231 (3%)

Query: 22  GGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDG-EPIQQLQP 80
           G IKA+ +  + V +G I G+IG +G+GKT+L  +L      D G++  DG E      P
Sbjct: 17  GEIKALNDINLNVEEGEIVGIIGMSGSGKTSLLRILRGVEPFDSGKITLDGIEVSPDSSP 76

Query: 81  HQIAQQGMVRTFQVARTLSRL--SVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQE 138
           +  A+        + R+      + L+N++   +K  G  +    LQ   V     +  +
Sbjct: 77  YYFAKLKKATAIHLQRSFGLWGETALQNVV---RKLAGAKYGDESLQD--VDDAVAEFGD 131

Query: 139 QAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDI 198
           QA  +LE VGL  K   +A  LSGG+++ L M R L   PK++LLDEPA    PR   +I
Sbjct: 132 QAKEILEIVGLGHKINHFAPVLSGGEKQRLIMARQLAKKPKVLLLDEPATMSCPRTKQEI 191

Query: 199 CDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249
            D I   N++ G+T +++ H  +V   L DR+ ++  G+ + +G+  EI T
Sbjct: 192 LDAIKNINKELGVTIVLVSHLPEVHRYLSDRLVLMENGEIIDEGSTEEIIT 242



 Score = 69.3 bits (168), Expect = 2e-16
 Identities = 54/278 (19%), Positives = 120/278 (43%), Gaps = 58/278 (20%)

Query: 22  GGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQPH 81
           G    +++   ++ +G I  LIGP+GAGKT L  +++    PD G ++F      +L  +
Sbjct: 280 GNTLQIKDVNFDIKKGEIVSLIGPSGAGKTVLLRMIAGLDAPDSGSILF------KLDDN 333

Query: 82  QIAQQGM-VRTFQVARTL--------------------SRLSVLENMLLAAQKQTGENFW 120
            +  Q + +    V R L                    +RL V +  +++  ++T E   
Sbjct: 334 WVDMQDLGLERMNVRRKLGFMHQEFALTHYATIKDQIAARLGVKDEHVISKARKTAEELG 393

Query: 121 -------------------------QVQLQPQVVVK-----EEKQLQEQAMFLLESVGLA 150
                                    +++L+P ++        + ++++ A  + +++ L 
Sbjct: 394 ISDKILDVLYQLTDLPEHEAKARLEKIELKPDILDLLFPKFPDTEVRKYAEPIFKALDLP 453

Query: 151 KKAYEYAG-GLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDICDRILTWNRQD 209
               +     LSGGQ+    +   L + P +++LDEP   ++P  +  + + +   N++ 
Sbjct: 454 LDILDRCSYELSGGQKVRATLALVLTSKPDVLILDEPFGDLDPITLRIVSNSLKRINKEF 513

Query: 210 GMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEI 247
             T L++ H++D I  +  R  ++ +G+ + DG P ++
Sbjct: 514 NTTILMVSHHVDFIREVTTRAIMIEDGKLVGDGDPQKL 551


Lambda     K      H
   0.319    0.136    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: 269
Number of extensions: 11
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 260
Length of database: 566
Length adjustment: 30
Effective length of query: 230
Effective length of database: 536
Effective search space:   123280
Effective search space used:   123280
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 (21.7 bits)
S2: 50 (23.9 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