GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Paraburkholderia bryophila 376MFSha3.1

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate H281DRAFT_00360 H281DRAFT_00360 hypothetical protein

Query= metacyc::MONOMER-20676
         (396 letters)



>FitnessBrowser__Burk376:H281DRAFT_00360
          Length = 402

 Score =  427 bits (1099), Expect = e-124
 Identities = 212/404 (52%), Positives = 281/404 (69%), Gaps = 10/404 (2%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           MDLNF+ EE AFR+EV  F +D +P     K+  GR  T+++M  W+ ILN++GW   HW
Sbjct: 1   MDLNFTPEEEAFREEVLAFLRDKLPQHLADKVHGGRRLTRDDMAGWHAILNERGWLANHW 60

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           P EYGG GW++VQ +IF  E   A AP+ + FGV+M+GPV+  +GSE QK+ +LPRI + 
Sbjct: 61  PAEYGGPGWTAVQKFIFENECALAGAPRIVPFGVNMLGPVLIRYGSESQKRHWLPRILDG 120

Query: 121 DDWWCQGFSEPGSGSDLASLKTKA----EKKGDKWIINGQKTWTTLAQHADWIFCLCRTD 176
            DWWCQG+SEPG+GSDLAS+KT A    +  G+ +I+NGQKTWTTL  +A+ IFCL RT 
Sbjct: 121 SDWWCQGYSEPGAGSDLASVKTTAVRGVDADGEHYIVNGQKTWTTLGHYANMIFCLVRTA 180

Query: 177 PAAKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDY 236
              +KQEGISF+L+DMKT G+ VRPI T+DG HEVNEVFF DV VP ENLVG+ENKGW Y
Sbjct: 181 TDVRKQEGISFLLIDMKTPGVEVRPIITLDGEHEVNEVFFTDVRVPAENLVGEENKGWTY 240

Query: 237 AKFLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALE 296
           AK+LL  ERT IA VG S   + R++++AA+ +  G+P+ EDP F  ++A VEI+L+ ++
Sbjct: 241 AKYLLTYERTNIAGVGFSVAAVNRLRKIAAKQQRNGRPLCEDPAFAARMARVEIDLENMK 300

Query: 297 LTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSN 356
            T LRV+A     G G P   SS+LKI+G+EI+Q  + L    +GP+A P+      D  
Sbjct: 301 TTNLRVIA--AVAGGGVPGAESSMLKIRGTEIRQEISSLTRRAMGPYAQPFIEEALHDGY 358

Query: 357 ETM----DWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
           +      +  A  A  YFNNRK+SI+GGSNEIQ+NII K +LGL
Sbjct: 359 QGAPVGPEEAASAASLYFNNRKLSIFGGSNEIQKNIISKMILGL 402


Lambda     K      H
   0.317    0.135    0.411 

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: 503
Number of extensions: 14
Number of successful extensions: 4
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: 396
Length of database: 402
Length adjustment: 31
Effective length of query: 365
Effective length of database: 371
Effective search space:   135415
Effective search space used:   135415
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 (21.6 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