Alignments for a candidate for paaH in Xanthobacter autotrophicus Py2

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Xanthobacter autotrophicus Py2

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_012112925.1 XAUT_RS04535 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_000017645.1:WP_012112925.1
          Length = 704

 Score =  610 bits (1573), Expect = e-179
 Identities = 338/686 (49%), Positives = 442/686 (64%), Gaps = 10/686 (1%)

Query: 15  RGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFG 74
           +GKV ++ ID APVNALS  VR+GLL A+   +AD  V A++I G    FIAGADIRE  
Sbjct: 17  QGKVGVIAIDFAPVNALSKAVRQGLLDAVRTLEADPDVAALVISGGPGRFIAGADIREMS 76

Query: 75  KPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLG 134
           +PP  P LPDV   ++AC KPVVAAI GAALGGG E+ALA   R+    A +GL E +LG
Sbjct: 77  QPPDAPFLPDVVAAVDACAKPVVAAIAGAALGGGCEIALACDLRLGGPKALVGLTETRLG 136

Query: 135 LLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHE 194
           L+PGAGGTQR P L+G   A+ LI  GR   A +ALA GL+D +   D +LA  +A    
Sbjct: 137 LIPGAGGTQRLPCLVGVAQAIALICEGRVLKAGDALALGLLDEVVEGD-LLATAIA---- 191

Query: 195 LLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFD 254
                AP    R  +AL   A   AA   A A   K ++G+ +  + +  + AA E  F 
Sbjct: 192 ----RAPGMPKRRLSALPVPARDAAAEEAAAARARKAAKGVPAIDEAIRVIRAAGEGDFA 247

Query: 255 EGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIGVVGGGTMGAG 314
            GL +ER  FL   +S +   L H FFAERE  K P      PR +  + V+G GTMGAG
Sbjct: 248 SGLALERAAFLALRESAEAKALRHLFFAEREAGKVPGLEGVAPRPVEAVAVIGAGTMGAG 307

Query: 315 IAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSY 374
           IA+A+ DAGL VT+IERD  + A G   +  +Y   +  GRL+  + A   +R + +  +
Sbjct: 308 IAMALADAGLAVTLIERDAEAAAAGFQRVSDLYARQVKSGRLTDAQGAERRARVTATADW 367

Query: 375 DALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVI 434
             L+  DLV+EA FED+AVK  +F  LD V K GAVLATNTSYLD+DA+A++ SRP DV+
Sbjct: 368 GRLSAVDLVVEAAFEDMAVKADIFRRLDAVAKPGAVLATNTSYLDLDAIAAATSRPQDVV 427

Query: 435 GLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYR 494
           GLHFF+PAN+MKLLEVV P + + DV+ATA  LAK++ K PV AG CDGFIGNR+ A+YR
Sbjct: 428 GLHFFAPANVMKLLEVVRPARSAPDVIATALALAKRMGKQPVVAGNCDGFIGNRIYALYR 487

Query: 495 SAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQ 554
             A+ ++EDG SP ++DAA+ A+GF MG F V D++G DI +A RKRRAATR+PA RYV 
Sbjct: 488 RHAEVLVEDGTSPQEVDAALEAYGFAMGLFAVSDMSGLDIAYAMRKRRAATRDPAERYVA 547

Query: 555 IADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIR 614
           IADRL E+G  G+K+G G+Y Y + + + T DP VEA+I   RA  GITPR+F+  +I R
Sbjct: 548 IADRLVEQGRLGRKTGAGWYAY-DAAGAKTCDPVVEAVIAEARAEKGITPRAFSAGQIQR 606

Query: 615 RYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIRE 674
           R +A M NEGA  + E IALR  D+D+ F++GYGFPR +GGPM  AD +GL  +L ++  
Sbjct: 607 RLLAVMANEGAKALAEGIALRASDIDLAFVHGYGFPRTKGGPMWAADQMGLRAVLTEVEA 666

Query: 675 FAKEDPLFWKPSPLLIELVERGADFA 700
                    +P+PLL+ L   G  FA
Sbjct: 667 AHAAGGAGSEPAPLLVALARDGHSFA 692


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: 1148
Number of extensions: 52
Number of successful extensions: 4
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: 704
Length adjustment: 39
Effective length of query: 667
Effective length of database: 665
Effective search space:   443555
Effective search space used:   443555
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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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