GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Marinobacter adhaerens HP15

Align 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Gamma-aminobutyraldehyde dehydrogenase; EC 1.2.1.47; EC 1.2.1.3; EC 1.2.1.19 (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase

Query= SwissProt::Q9JLJ3
         (494 letters)



>FitnessBrowser__Marino:GFF3684
          Length = 489

 Score =  503 bits (1296), Expect = e-147
 Identities = 256/475 (53%), Positives = 334/475 (70%), Gaps = 8/475 (1%)

Query: 25  ASGTEKAF---EPATGREIATFKCSGEKEVNLAVENAKAAFKIWSKKSGLERCQVLLEAA 81
           A+ T + F    PATG+ I   + + E     A+E+A+A F  WS  + +ER ++LL A 
Sbjct: 18  ANSTGETFPVVNPATGQVIYEVEVADESVQQAAIESARAGFAEWSAMTAIERSRILLRAV 77

Query: 82  RIIKERRDEIAIMETINNGKSIFEAR-LDVDTSWQCLEYYAGLAASMAGEHIQLPGGSFG 140
            I++ER DE+A  E  + GK   EA  +DV T    +E++AGLA S+ G    L GG F 
Sbjct: 78  AILRERNDELAAAEVRDTGKPWQEAEAVDVVTGADAVEFFAGLAPSIEGNQQDL-GGDFY 136

Query: 141 YTRREPLGVCLGIGAWNYPFQIACWKSAPALACGNAMIFKPSPFTPVSALLLAEIYTKAG 200
           YTRREPLG+C GIGAWNYP QIACWKSAPALACGNAMIFKPS  TP+ A+ LAEI+T+AG
Sbjct: 137 YTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPSEETPMGAVKLAEIFTEAG 196

Query: 201 APNGLFNVVQGGAATGQFLCQHRDVAKVSFTGSVPTGMKIMEMAAKGIKPITLELGGKSP 260
            P G+FNVVQG A  GQ+L  H ++AKVSFTG V TG K+M  A+  +K +T+ELGGKSP
Sbjct: 197 VPAGVFNVVQGAAEVGQWLTHHPEIAKVSFTGEVATGKKVMAAASSTLKDVTMELGGKSP 256

Query: 261 LIIFSDCNMKNAVKGALLANFLTQGQVCCNGTRVFVQKEIADAFTKEVVRQTQ-RIKIGD 319
           LIIF D +++NA+  A++ NF TQG++C NGTRVFV +++   F + ++ +T+  IK GD
Sbjct: 257 LIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFIERLLERTRNNIKPGD 316

Query: 320 PLLEDTRMGPLINAPHLERVLGFVRSAKEQGATVLCGGEPYAPEDPKLKHGYYMTPCILT 379
           P+  DT  G LI+A H + VL ++     +GAT+  GG  + PED   K GY++ P I T
Sbjct: 317 PMNPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDS--KGGYFVEPTIFT 374

Query: 380 NCTDDMTCVKEEIFGPVMSILTFETEAEVLERANDTTFGLAAGVFTRDIQRAHRVAAELQ 439
           +CTDDMT VKEEIFGPVMS+LTF  E EV+ RAN+T  GLAAGVFT DI+RAHRV  ++Q
Sbjct: 375 DCTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAGVFTNDIRRAHRVIHQIQ 434

Query: 440 AGTCYINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494
           AG C+IN+Y  SP E+P GGYK SG GRENGR TI +Y+Q+K+V V M D+++ F
Sbjct: 435 AGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYVGMEDLDAPF 489


Lambda     K      H
   0.319    0.136    0.408 

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: 754
Number of extensions: 44
Number of successful extensions: 5
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: 494
Length of database: 489
Length adjustment: 34
Effective length of query: 460
Effective length of database: 455
Effective search space:   209300
Effective search space used:   209300
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: 52 (24.6 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