Alignments for a candidate for paaH in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Stenotrophomonas chelatiphaga DSM 21508

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_057506695.1 ABB28_RS00235 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_001431535.1:WP_057506695.1
          Length = 790

 Score =  882 bits (2280), Expect = 0.0
 Identities = 463/810 (57%), Positives = 574/810 (70%), Gaps = 23/810 (2%)

Query: 1   MSNFI-VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLS 59
           MSN + V++ AVLGAGVMGAQIAAHL NA V  VLFDLPAK+GP +G+ ++AI NL KLS
Sbjct: 1   MSNSLPVRRAAVLGAGVMGAQIAAHLTNAGVDTVLFDLPAKDGPADGVVIKAIANLTKLS 60

Query: 60  PAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFA 119
           PAPL  K  A  I  ANYE  +  L++CDL+IEAIAERMDWK DLYKK+AP +A HA+ A
Sbjct: 61  PAPLASKSYAESITPANYETGLEQLRDCDLIIEAIAERMDWKQDLYKKIAPFVADHAVLA 120

Query: 120 TNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTT 179
           +NTSGL I  L+D     L+ RFCGVHFFNPPRYMHL ELIP  TT   +L+ LEAFL T
Sbjct: 121 SNTSGLGINKLADVLPEQLRHRFCGVHFFNPPRYMHLAELIPATTTDASVLEALEAFLVT 180

Query: 180 TLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRT 239
           TLGKGVV AKDTPNFI NR+G+FSIL+     ++FG+ FD VD LTG  +GR KSAT+RT
Sbjct: 181 TLGKGVVYAKDTPNFIGNRIGVFSILSTIHHTQEFGLGFDEVDGLTGPLVGRPKSATYRT 240

Query: 240 ADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAI 299
           +DVVGLDTMAHVIKTM DTL +DP+   +K+P  L  L+  GALGQKTGAG ++K GK I
Sbjct: 241 SDVVGLDTMAHVIKTMGDTLPNDPWHEFFKSPKWLDALISKGALGQKTGAGIFRKAGKDI 300

Query: 300 KVLDAKTGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQFLWAVFRDVFHYIA 358
            VLD +   Y  A + A   VV +LK K+ AE+   LRES +PQAQFLWA FRD+FHY A
Sbjct: 301 VVLDLEKQDYRPADRAAAPEVVEILKIKNPAEKFAKLRESQHPQAQFLWATFRDLFHYSA 360

Query: 359 VYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPA 418
            +L  IA +A D+DLAIRWG+GW+ GPFE WQ+AGWKQVA+W+ +D+ AGK++S+APLP 
Sbjct: 361 YHLADIAETARDVDLAIRWGYGWSLGPFETWQAAGWKQVAQWIADDIVAGKSMSSAPLPD 420

Query: 419 WVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTV 478
           WVF+G      GVHAA GS+SP+  + + RS LPVYQRQ F   + G   A     G TV
Sbjct: 421 WVFDG----RDGVHAAEGSYSPSRNAKLPRSALPVYQRQRFPDPLLGETFA----PGETV 472

Query: 479 EENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538
            END VR+W     D + VVSFK+KMNT+   V+DGL  AI  AE  +KGLV+WQ     
Sbjct: 473 FENDGVRMW--HDGDGIAVVSFKTKMNTVSDHVLDGLQEAIKRAEQDFKGLVIWQQKE-- 528

Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598
                 PFSAGA+L  A+     G  +  E  V  FQ     +KY+ VPVV+A  G+ALG
Sbjct: 529 ------PFSAGADLAGALGLLQAGKVEQFEEMVHNFQRTSQAIKYSLVPVVTAVRGLALG 582

Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLT 658
           GGCE  +HSA  VA+LE+YIGLVE GVGL+PAGGGLKE A+ A++AA   G  ++   L 
Sbjct: 583 GGCEFQMHSAKSVASLESYIGLVEAGVGLLPAGGGLKELAVRASQAAGPGG--DVFAELK 640

Query: 659 SRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT- 717
             F++ AMAKVS SA+ A+++G ++ +DK+VFN +E LY+A+ EVRALA  GYR P+P  
Sbjct: 641 KTFETVAMAKVSNSAVNAQELGLMRATDKVVFNSYEALYIAKAEVRALAEGGYRPPMPAR 700

Query: 718 LVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLAL 777
            + VAG  GIAT K  LVNM +G FIS +D+ IA RIA  +CGG+V+ G+LV E+WLL L
Sbjct: 701 RIQVAGDVGIATFKMMLVNMLEGRFISPYDYEIAVRIATVLCGGEVDRGTLVDEEWLLTL 760

Query: 778 ERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           ERK FV+L    KTQ RI  ML+TGKP+RN
Sbjct: 761 ERKHFVELAQQEKTQARIAHMLKTGKPLRN 790


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: 1575
Number of extensions: 77
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: 790
Length adjustment: 41
Effective length of query: 766
Effective length of database: 749
Effective search space:   573734
Effective search space used:   573734
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 24 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