Alignments for a candidate for paaH in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Paraburkholderia phymatum STM815

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_012400431.1 BPHY_RS05220 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_000020045.1:WP_012400431.1
          Length = 694

 Score =  587 bits (1513), Expect = e-172
 Identities = 311/688 (45%), Positives = 442/688 (64%), Gaps = 8/688 (1%)

Query: 18  VLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPP 77
           + ++T+++ PVN L    R G++  I+ A  D AV+A+++ GAG+ F  GADI EF  P 
Sbjct: 11  IAVITLNNPPVNGLGLSTRMGIVEGIDRAQHDPAVKAIVLTGAGKAFSGGADITEFNTPK 70

Query: 78  V--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGL 135
               P+L  V   +E   KPVVAAIH  A+GGGLE+AL AHYR+A  GA++ LPEV+LG+
Sbjct: 71  AFQEPTLATVIKAVEGSAKPVVAAIHSVAMGGGLELALGAHYRVAAPGAQIALPEVKLGI 130

Query: 136 LPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHEL 195
           LPGAGGTQR PR +G +AAL++I+SG    +++     + D++   + +L + LA+  ++
Sbjct: 131 LPGAGGTQRLPRALGLEAALNMIVSGTPVMSEKLAGTPMFDQMVEGN-LLEDALAFARKV 189

Query: 196 LAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDE 255
            A   P  + RD       AA    +  AR   A  ++   +P K +DA+EA + + FD 
Sbjct: 190 GAQSGPHPKIRDRNIGHPNAAGF--IQFARNSVAGVAKQYPAPHKCIDAIEAGVLKGFDH 247

Query: 256 GLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGVVGGGTMGAG 314
           G++VER+ FL  + +P+   L HAFF ER   K P+  +  P R ++ +GV+G GTMG G
Sbjct: 248 GVKVERECFLALVQTPESKALRHAFFGERAASKIPDVPSDTPARNIDKVGVIGAGTMGGG 307

Query: 315 IAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSY 374
           IA+  ++AGLPVT++E    +L RG A I K Y+  + KG+L+ E     MS  + + +Y
Sbjct: 308 IAMNFVNAGLPVTLLEMKQDALERGLATIRKNYEATVKKGKLTMEALEQRMSLITPTLTY 367

Query: 375 DALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVI 434
           +AL  ADL+IEAV+E+L VK+ VF  LD V K GA+LA+NTS LD++ +A+   RP DV+
Sbjct: 368 EALGDADLIIEAVYEELGVKEQVFTRLDEVAKPGAILASNTSTLDLNKIAAFTKRPQDVV 427

Query: 435 GLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYR 494
           G+HFFSPAN+MKLLEVV  K  + DV+AT  ++AKK+RKT V +GVCDGFIGNR++  Y 
Sbjct: 428 GMHFFSPANVMKLLEVVRGKDTAKDVLATVMQVAKKIRKTAVVSGVCDGFIGNRMVEQYV 487

Query: 495 SAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQ 554
             A  M+E+GA P Q+D A+  FGF MGPF++ DLAG DIGWA RKRR     P  RY +
Sbjct: 488 RQALFMLEEGALPAQVDKAIEKFGFAMGPFRMSDLAGNDIGWAIRKRR-YQEEPHMRYSK 546

Query: 555 IADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIR 614
           IADRLCE G FGQK+G G+Y Y  G R+  P   ++ +I A     GI  R  +D+EI+ 
Sbjct: 547 IADRLCEAGRFGQKTGGGWYDYKAGDRNAYPSKPIDEMIVAHSKELGIERRKISDDEIVE 606

Query: 615 RYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIRE 674
           R + A++NEGA ++ E IA +  D+D+ +L GYGFP +RGGPM YAD VGL  +   IR 
Sbjct: 607 RLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLWRGGPMLYADSVGLYNVERAIRR 666

Query: 675 FAKE-DPLFWKPSPLLIELVERGADFAS 701
           +A + +   W+ +  ++E   +G  F S
Sbjct: 667 YAAQPNGDAWQIAAGIVERAAQGRGFNS 694


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: 1083
Number of extensions: 52
Number of successful extensions: 5
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: 694
Length adjustment: 39
Effective length of query: 667
Effective length of database: 655
Effective search space:   436885
Effective search space used:   436885
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