GapMind for catabolism of small carbon sources

 

Alignments 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:

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:

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:

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:

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