GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Limnohabitans curvus MWH-C5

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_108402938.1 B9Z44_RS14295 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_003063475.1:WP_108402938.1
          Length = 682

 Score =  484 bits (1247), Expect = e-141
 Identities = 276/670 (41%), Positives = 384/670 (57%), Gaps = 15/670 (2%)

Query: 10  VSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGAD 69
           V  +++  V ++T+D+ PVNA+S  VRRGL++A+   +   A  AVL VG+   FIAGAD
Sbjct: 7   VQGQVKQGVYVITLDNPPVNAISISVRRGLISAVNDFEQSNAQVAVL-VGSNGTFIAGAD 65

Query: 70  IREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLP 129
           I EF +    P L DV   IE C KP+VAA+ GA LGGGLEVALA   RIA     +GLP
Sbjct: 66  IHEFARTSDGPVLLDVVRVIENCKKPIVAALQGAVLGGGLEVALACDARIAHVDTVIGLP 125

Query: 130 EVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGL 189
           EV LG++PGAGGTQ  PR IG   A+D+I   +  SA+EA    L+D +  SD ++A  L
Sbjct: 126 EVSLGIIPGAGGTQLLPRRIGISRAIDIICGAQRLSAEEAKHLRLVDSVVCSDILVAANL 185

Query: 190 --AYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEA 247
               +    +    +    D A +         +   R   AK           +D ++A
Sbjct: 186 FARNIEHKSSVRDELVPNEDPALIDQAINRYTKLGRCRPAIAKA----------IDLIQA 235

Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIGVVG 307
           A   P +EGL +E   FLE   S +   L H FFAE+   K P+T+   P  +NT+ V+G
Sbjct: 236 AARLPIEEGLVLESAAFLELRKSQEAQALRHLFFAEKTCRKPPQTKEVAPIPINTVCVIG 295

Query: 308 GGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSR 367
            GTMG GIA+ +LDA   V ++E+D  +L +G   I   Y   +  G+LS  + +  +S 
Sbjct: 296 AGTMGTGIAICLLDAEFSVMLLEQDKEALDKGEERIFSHYQKQVETGKLSPVEASKCLSH 355

Query: 368 WSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSV 427
              S +++ LA ADLVIEAV+ED+ VKQ VF ++D+     A+LATNTSYL +D +A + 
Sbjct: 356 LLCSLNWEELAKADLVIEAVYEDMLVKQDVFKKIDQFANPNAILATNTSYLSVDKIALAT 415

Query: 428 SRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGN 487
           +RP  VIGLHFFSPAN+MKLLE+V  KQ   + +        +L K PV      GFIGN
Sbjct: 416 TRPKRVIGLHFFSPANVMKLLEIVNAKQTCLETLHAVIAFGNRLNKYPVVTKDSFGFIGN 475

Query: 488 RVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRN 547
           R+   YR+  + M+EDGA P ++DAA+  FG  MGPF V DL+G DI W  R R+   +N
Sbjct: 476 RIYNAYRTQCEFMLEDGAWPEEVDAALVDFGMAMGPFTVADLSGLDIAW--RMRKTQRKN 533

Query: 548 PAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSF 607
              RYV I D LCE G FG+K+  G+Y Y  G +       V  II+    R  I  R+ 
Sbjct: 534 QETRYVDILDTLCELGRFGRKTSAGYYDYTNGKKQANTSELVRQIIENASQRRRIKRRTL 593

Query: 608 TDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPK 667
             + I  R + +M+NE A ++ E +A R  D+DV F++GYGFPR++GGP+ +A      +
Sbjct: 594 NSKHIQNRALLSMVNEAALLMREGVAQRASDIDVVFVHGYGFPRWQGGPVFWARQQDRQQ 653

Query: 668 ILADIREFAK 677
           + +DI   A+
Sbjct: 654 LQSDIAGLAE 663


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: 918
Number of extensions: 34
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: 682
Length adjustment: 39
Effective length of query: 667
Effective length of database: 643
Effective search space:   428881
Effective search space used:   428881
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:

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