Alignments for a candidate for paaH in Xenophilus azovorans DSM 13620

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Xenophilus azovorans DSM 13620

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_051953766.1 Q392_RS19230 3-hydroxyacyl-CoA dehydrogenase

Query= reanno::BFirm:BPHYT_RS13545
         (706 letters)



>NCBI__GCF_000745855.1:WP_051953766.1
          Length = 686

 Score =  568 bits (1463), Expect = e-166
 Identities = 305/656 (46%), Positives = 413/656 (62%), Gaps = 8/656 (1%)

Query: 9   VVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGA 68
           VV  E  G+VLL+ ID+ P+NA SA VR GL+ A+  A+AD  + A +I+GAG  F+AG+
Sbjct: 6   VVRCEREGEVLLILIDNPPINAGSAPVRAGLVDAVAQAEADSEIRAAVIMGAGNTFVAGS 65

Query: 69  DIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGL 128
           D+REFG+P   P LP V   IE C KP+VAA+HGAALGGG E+AL    R+A+ G  +GL
Sbjct: 66  DLREFGQPLQDPQLPAVIEAIERCGKPIVAALHGAALGGGFELALGCDARVALRGTVVGL 125

Query: 129 PEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEG 188
           PEV LG++PGAGGTQR PRL+G   AL +I SG    A EAL  G+ID +  +D +    
Sbjct: 126 PEVTLGIIPGAGGTQRLPRLVGRPRALKMICSGERVGAAEALVSGIIDAVVDAD-LRTAA 184

Query: 189 LAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAA 248
           L Y  E+ A     RR RD    +D AA+    AT      K  R   +    + AV + 
Sbjct: 185 LRYASEMGAK----RRVRDLPVPADDAAAFEEAAT---RALKAGRNRPNVAAAIVAVRST 237

Query: 249 IEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIGVVGG 308
             + FDEGL  ER+ F     +P    L H FFAER+  +        P+ ++++ V+G 
Sbjct: 238 GARDFDEGLYQEREAFQALRVAPDAFALRHLFFAERQSARPAPLEGTDPKAVHSVAVIGA 297

Query: 309 GTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRW 368
           GTMG+GIA+A LDAG  V ++E+D  +L RG   + K Y   +A G+L+ E+ A    R 
Sbjct: 298 GTMGSGIAIAALDAGCQVLLVEQDADALQRGTDRVNKHYASRVAAGKLAKERAADCEQRM 357

Query: 369 SGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVS 428
           + +  +  +  ADL+IEAVFEDLA+K+ VF  LD V + GAVLA+NTSYLD+DA+A++  
Sbjct: 358 APTLDWARIREADLIIEAVFEDLAIKRTVFERLDGVARPGAVLASNTSYLDLDAIAAATG 417

Query: 429 RPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNR 488
           RP DVIGLHFFSPA +M+L+EVV   + SA  +AT  +L K++ K PV      GFIGNR
Sbjct: 418 RPQDVIGLHFFSPAQVMRLVEVVGGAKSSAQALATGVQLTKRMGKLPVLTRNAFGFIGNR 477

Query: 489 VLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNP 548
           + A YR   + M+E+GA P  +DAA+ A+GF MGPF V D++G DI W  R+ +AA R+P
Sbjct: 478 IYAAYRRQCEFMLEEGAYPRDVDAALEAWGFAMGPFAVADMSGLDIAWRMRQAQAARRDP 537

Query: 549 AARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFT 608
           AARYV+I DRLCERG  G+K+G G+Y YPEG      D  V A+ID      G+  RS  
Sbjct: 538 AARYVEIPDRLCERGRLGRKTGLGYYAYPEGGARPQVDAAVHALIDEASRAKGLVRRSLA 597

Query: 609 DEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVG 664
            EE+ RR + +M+NE A +V E +A +  DVD+  + GYGFPR++GGP+ +A   G
Sbjct: 598 AEEVQRRALLSMVNEAALLVAEGVAFQTADVDLVLVNGYGFPRWQGGPVWWARQRG 653


Lambda     K      H
   0.320    0.136    0.392 

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: 1160
Number of extensions: 61
Number of successful extensions: 2
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: 706
Length of database: 686
Length adjustment: 39
Effective length of query: 667
Effective length of database: 647
Effective search space:   431549
Effective search space used:   431549
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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