GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Pedobacter sp. GW460-11-11-14-LB5

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= BRENDA::B6ECN9
         (505 letters)



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  327 bits (838), Expect = 6e-94
 Identities = 199/486 (40%), Positives = 283/486 (58%), Gaps = 26/486 (5%)

Query: 14  FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73
           +I G++  P+K      I+P + ++      +T+ED+++AV AA  A +   W  T+  +
Sbjct: 17  YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKT--WSKTSSTE 74

Query: 74  RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEA-ASDIDDVVACFEYYADLAEA----L 128
           R+  L  IA ++ +    LA +ETIDNGK   E  A+D+   V  F Y+A +  A    L
Sbjct: 75  RSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSL 134

Query: 129 DSKKQTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSE 188
               Q  V L        ++ EP+GVV  I PWN+PLLM  WK+APALAAG   +LKP+E
Sbjct: 135 SELDQNTVSL--------IVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAE 186

Query: 189 LASITSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMT 248
              ++ + L E+  ++ LPPG ++++ G G E G  LV++P V K AFTGS PTG  +M 
Sbjct: 187 STPVSIMVLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQ 245

Query: 249 AAAQLVKPVTLELGGKSPIVVF-----DDIHNLDTAVEWTLFGCFWTNGQICSATSRLII 303
            A + + PVTLELGGKSP + F     +D   LD AVE  +       G+IC+  SRL+I
Sbjct: 246 YATENIIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFAL-NQGEICTCPSRLLI 304

Query: 304 QETIAPQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYG 363
           QE I  +F+A+++E TK IKI  PL+    +G   S+ Q+EKI  +I   K+EGA +L G
Sbjct: 305 QEDIYEKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTG 364

Query: 364 G---DRPEHLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKF 420
           G   + P  L  GYYI+PTI       M I++EE+FGPVL V TFKT EEAIE+ANDT +
Sbjct: 365 GEINELPGELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLY 423

Query: 421 GLGAAILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENY 480
           GLGA + ++D     +  +A Q+G VW+N         P+GG K+SG GRE  +  L +Y
Sbjct: 424 GLGAGVWTRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHY 483

Query: 481 LNIKQV 486
              K +
Sbjct: 484 RQTKNM 489


Lambda     K      H
   0.318    0.136    0.421 

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: 624
Number of extensions: 31
Number of successful extensions: 8
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: 505
Length of database: 501
Length adjustment: 34
Effective length of query: 471
Effective length of database: 467
Effective search space:   219957
Effective search space used:   219957
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 (21.7 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