GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Galbibacter marinus ck-I2-15

Align Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_008990629.1 I215_RS03780 proline dehydrogenase

Query= reanno::Pedo557:CA265_RS11605
         (394 letters)



>NCBI__GCF_000300875.1:WP_008990629.1
          Length = 388

 Score =  399 bits (1024), Expect = e-115
 Identities = 188/384 (48%), Positives = 271/384 (70%)

Query: 11  FDNTEVAFRQKTNGELKKAYWLFKMIGSNFLTKVGPAITNFFLNIGLPIQGAIKATIFQQ 70
           FDNTE+AF+ K++ EL++AY+LFKMI    L ++G A+TNF +   LP++G I+AT+F  
Sbjct: 5   FDNTEIAFKLKSDSELERAYFLFKMIAHQPLVRIGTAVTNFAIKAHLPVEGLIRATVFDH 64

Query: 71  FCGGETIAECDKAIEQLHKGGVGTILDYSVEGEEEEQVFDETCAEIIRTIMRADGDVKIP 130
           FCGG +  +C K ++ +H  GV ++LDYSVEG E ++ FD   A  ++ +        IP
Sbjct: 65  FCGGVSELDCMKTVDAIHTAGVSSVLDYSVEGNENDEEFDAVVARTLKILDLVKEKQAIP 124

Query: 131 ITVFKITGIGRFALLQKLDAKETLNASEKAEYEKVKQRCEKICQTAFDKGVPIMIDAEET 190
             VFK T +GRF L  K+   +TL+  E+ E+++V  R E IC  A++  V ++IDAEE+
Sbjct: 125 FAVFKPTAVGRFDLYVKIGEGKTLDKEEQQEWDRVCLRYETICNKAYELDVALLIDAEES 184

Query: 191 WIQDTIDELALDMMRKFNRERIIVYNTYQMYRHDKLADMKADHLIAKADGFILGVKMVRG 250
           W+QD  DE+   MM+K+NR + IV+NT Q+YR +++  +K  H  AK DGF++G+K+VRG
Sbjct: 185 WMQDAADEIVEQMMKKYNRNKAIVFNTLQLYRWNRMDYLKGLHQRAKEDGFVVGMKLVRG 244

Query: 251 AYMEKERKRAAEMGYPSPIQPDKAASDRDYNESLRYCVDHIEEIAIVAGTHNEDSSRLLT 310
           AYMEKE  RA E GYP+PI   K A+D +YN ++ Y +DHI E+ +  G+HNE+S+ L  
Sbjct: 245 AYMEKENDRAEENGYPTPICESKKATDDNYNTAVGYMLDHIGELELFLGSHNEESTMLAL 304

Query: 311 YLLEEKNITHNHPHVYFAQLLGMSDNLSFNLADSNYNVAKYVPYGPIKAVMPYLFRRAQE 370
            +++EKN+  N   ++F QL GMSD++S+NLA+ NYNVAKY+P+GP++ VMPYL RRA+E
Sbjct: 305 NIMKEKNLAVNDSRIWFGQLYGMSDHISYNLANRNYNVAKYLPFGPVRDVMPYLIRRAEE 364

Query: 371 NTSVAGQTGRELGLIERELKRRKL 394
           NTSVAGQT REL L+ +E KRRKL
Sbjct: 365 NTSVAGQTTRELSLLSQERKRRKL 388


Lambda     K      H
   0.319    0.136    0.394 

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: 428
Number of extensions: 11
Number of successful extensions: 1
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: 394
Length of database: 388
Length adjustment: 31
Effective length of query: 363
Effective length of database: 357
Effective search space:   129591
Effective search space used:   129591
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: 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