Alignments for a candidate for paaH in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Dyella japonica UNC79MFTsu3.2

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate N515DRAFT_2687 N515DRAFT_2687 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2687
          Length = 798

 Score =  889 bits (2297), Expect = 0.0
 Identities = 468/808 (57%), Positives = 578/808 (71%), Gaps = 23/808 (2%)

Query: 2   SNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSPA 61
           S   ++K AVLGAGVMGAQIAAHL NA V  VLFDLPAKEGPK+GIAL+AIENLKKLSPA
Sbjct: 12  SKLRIRKAAVLGAGVMGAQIAAHLTNANVETVLFDLPAKEGPKSGIALKAIENLKKLSPA 71

Query: 62  PLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATN 121
           PL     A  I  ANY+DD+  LK+ DLVIEAIAERMDWK DLYKK+AP++A HA+ A+N
Sbjct: 72  PLADGSRAAAIIPANYDDDLEHLKDVDLVIEAIAERMDWKLDLYKKIAPYVAPHAVLASN 131

Query: 122 TSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTL 181
           TSGLSI  L++    +++ RF GVHFFNPPRYMHLVELIPT  T+ ++L+ LEAFLTT +
Sbjct: 132 TSGLSINGLAEALPEEMRHRFTGVHFFNPPRYMHLVELIPTRLTEAKVLEGLEAFLTTVV 191

Query: 182 GKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTAD 241
           GKGVV AKDTPNFI NR+G+FS+LA     E+F + FDVVD LTG  +GR KSAT+RTAD
Sbjct: 192 GKGVVYAKDTPNFIGNRIGVFSMLATMHHTEQFKLGFDVVDALTGPAVGRPKSATYRTAD 251

Query: 242 VVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIKV 301
           VVGLDTMAHVIKTM DTL DDP+   +K PA L+GL++ GALGQKTGAGFY+K GK I V
Sbjct: 252 VVGLDTMAHVIKTMADTLADDPWHQYFKAPAWLQGLIEQGALGQKTGAGFYRKAGKDIVV 311

Query: 302 LDAKTGQYVDAGKKA-DEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360
           LD     Y  + ++A DE+   +  KD AE+   LR S++PQAQFLWA FRD+FHY A +
Sbjct: 312 LDVAKRDYRASEQQASDEVAAILAIKDPAEKFAKLRASSDPQAQFLWATFRDLFHYTAYH 371

Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420
           L  IA +A D+D AIRWG+GW  GPFE WQ+AGW+QVA W+ ED+ AGKA+S+APLP WV
Sbjct: 372 LADIADTARDVDFAIRWGYGWKLGPFETWQAAGWQQVATWIGEDIAAGKAMSSAPLPKWV 431

Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480
            +G      GVH  +GS+S +  +   RS+ PVY+RQ F   I G    +    G TV E
Sbjct: 432 TDG----RSGVHGKSGSYSASANADKPRSQHPVYRRQLFPDPILG----EKFDQGSTVWE 483

Query: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLG 540
           ND VR+W + G D V ++SFK+KMNT+   V+DG+ +AID+AE   K +V+WQ       
Sbjct: 484 NDGVRLW-TLGDDGVGIISFKTKMNTVNDQVLDGIQQAIDVAEQQLKAVVIWQ------- 535

Query: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGG 600
             G PFSAGA+L+ A+     G     E  V  FQ   MR+K++ VPVVSA  G+ALGGG
Sbjct: 536 -TGEPFSAGADLKGALGLLQAGKLGDFEAMVANFQRTSMRIKHSLVPVVSAVRGLALGGG 594

Query: 601 CELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSR 660
           CE  +HSA  VAALE+YIGLVE GVGL+PAGGGL E A+ AA+A  A    +  + L   
Sbjct: 595 CEFQMHSARTVAALESYIGLVEAGVGLLPAGGGLHELAIRAAQANPA----DPFEALKKV 650

Query: 661 FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT-LV 719
           F++ AMAKVS SALEA+Q+G L+ SD +VFN +ELL+VA+    ALA +GYR PLP   +
Sbjct: 651 FETVAMAKVSGSALEAKQLGLLRDSDVVVFNAYELLHVAKQVAGALAESGYRPPLPARSI 710

Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779
           PVAG  G AT +ASL NM+ G F+S HD  IA+RIA+ +CGG +E GS V E+WLL LER
Sbjct: 711 PVAGDVGTATFRASLANMQAGYFVSEHDVAIATRIADTLCGGAIERGSQVDEEWLLQLER 770

Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           K FV+L  T KTQ RI   + TGKP+RN
Sbjct: 771 KHFVELAQTEKTQARIAHTMTTGKPLRN 798


Lambda     K      H
   0.319    0.134    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: 1652
Number of extensions: 72
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: 807
Length of database: 798
Length adjustment: 41
Effective length of query: 766
Effective length of database: 757
Effective search space:   579862
Effective search space used:   579862
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources