Aligments for a candidate for fadB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for fadB in Acidovorax sp. GW101-3H11

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate Ac3H11_2523 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2523
          Length = 699

 Score =  583 bits (1504), Expect = e-171
 Identities = 316/697 (45%), Positives = 445/697 (63%), Gaps = 14/697 (2%)

Query: 13  ELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIRE 72
           ++ G V ++T+ + PVN L    R+G++  +  A+AD AV++++I GAG  F  GADI+E
Sbjct: 6   KVHGSVAVITMANPPVNGLGLATRQGIVDGLGRANADAAVKSIVITGAGGAFSGGADIKE 65

Query: 73  FG--KPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPE 130
           FG  K    P+L  V   IE   KPVVAA+H  A+GGGLE+AL  HYRIA  G  + LPE
Sbjct: 66  FGTDKSLQEPNLLSVIAAIENSAKPVVAAMHSVAMGGGLELALGCHYRIAAPGCSIALPE 125

Query: 131 VQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFG---LIDRLGSS-DDILA 186
           V+LGL+PGAGGTQR PR+IG +AAL+LI+SG    ++   A     L D++ +S + + A
Sbjct: 126 VKLGLIPGAGGTQRLPRVIGVEAALNLIVSGEPVKSEMIGAVPGQKLFDKMAASAESLAA 185

Query: 187 EGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVE 246
           E LA+   +  A  P+   R+           A    AR      ++   +P K VDAVE
Sbjct: 186 EALAFAQSVADAR-PLPLVRNFPCKHSEGD--AYFQFARNMVKGMAKNFPAPAKCVDAVE 242

Query: 247 AAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGV 305
           AA ++ F EG+ VER++F+  + +P+   L H F AER   K P+  +  P R +  +GV
Sbjct: 243 AATKKKFAEGMLVEREIFINLMWTPESRALRHLFMAERAASKIPDVASDTPKRDIKLVGV 302

Query: 306 VGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALM 365
           +G GTMG GI++  L+AG+PV ++E    +L RG A I+K Y+  + KG+L  +K    M
Sbjct: 303 IGAGTMGGGISMNFLNAGIPVKILEMKQEALDRGVATIKKNYEAQVKKGKLKQDKYDQRM 362

Query: 366 SRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALAS 425
           +  S + SYD     DL+IEAVFE++ VK+AVF +LD V K GA+LA+NTS LD+D +A+
Sbjct: 363 ALLSTTLSYDDFKDCDLIIEAVFEEMGVKEAVFKQLDAVAKPGAILASNTSTLDVDKIAA 422

Query: 426 SVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFI 485
              RP DV+G+HFFSPAN+MKLLEVV  K+ + DV+AT   + KK++KT V +GVCDGFI
Sbjct: 423 FTKRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMAIGKKIKKTSVVSGVCDGFI 482

Query: 486 GNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAAT 545
           GNR++  Y   A  ++++G +P Q+D AV  FGF MGPF++ DLAG DIGWA RKRR+  
Sbjct: 483 GNRMIEQYSRQAGFLLDEGCTPQQVDKAVEKFGFAMGPFRMGDLAGNDIGWAIRKRRSVE 542

Query: 546 RNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPR 605
           R    +Y + AD+LCE G FGQK+G G+Y Y  G R   P   V  +I+  R   GITPR
Sbjct: 543 R-ADMKYSRTADKLCELGRFGQKTGAGWYDYQAGKRDAIPSDLVNKMIEDHRKELGITPR 601

Query: 606 SFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGL 665
             +DEEI++R + A++NEGA+++ + IA +  D+D+ +L GYGFP +RGGPM YA  VGL
Sbjct: 602 KISDEEIVQRLVFALVNEGAHILEDGIASKSGDIDMVYLTGYGFPIHRGGPMHYASEVGL 661

Query: 666 PKILADIREFAK---EDPLFWKPSPLLIELVERGADF 699
             ++  +  FA+   +D  FWKP+PLL +L   G  F
Sbjct: 662 FNVVQAMDRFARNPLDDAAFWKPAPLLAKLAAEGKAF 698


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: 1021
Number of extensions: 30
Number of successful extensions: 6
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: 699
Length adjustment: 39
Effective length of query: 667
Effective length of database: 660
Effective search space:   440220
Effective search space used:   440220
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 17 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, or view the source code.

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