Alignments for a candidate for fadB in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Rhodomicrobium vannielii ATCC 17100

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_013420474.1 RVAN_RS14570 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_000166055.1:WP_013420474.1
          Length = 695

 Score =  594 bits (1531), Expect = e-174
 Identities = 318/686 (46%), Positives = 438/686 (63%), Gaps = 7/686 (1%)

Query: 10  VSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGAD 69
           V+ E +  V ++T+D+ P+N +S +VR GL+ AI  A+AD   +AV+++GAGRNF AGAD
Sbjct: 6   VTYETKDGVGVITVDNPPLNVVSNEVRDGLMLAIRKAEADPVAKAVVLIGAGRNFAAGAD 65

Query: 70  IREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLP 129
           I E   P     + D+C  +E   KPVVAA+HG  +  GLEVALA HYRIA   A+LGLP
Sbjct: 66  IYELTHPYSGADINDICAALEDLPKPVVAALHGTPVARGLEVALACHYRIAAKDARLGLP 125

Query: 130 EVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE-G 188
           EV++GLLPG GGTQR PRL+GA+AALD+I+SG    A +A   GL+D +   D + A   
Sbjct: 126 EVKVGLLPGGGGTQRLPRLVGAKAALDIIISGDLVPAVKAKTIGLVDEVVDGDILPAAIA 185

Query: 189 LAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAA 248
           LA     L+ H P  R   A    DR + L      R E  ++     +  + VDA+E+A
Sbjct: 186 LAKSKSFLSKH-PKTRELSAKIAPDRGSHL--FEGRRDELRRRQPFQHAQFRCVDAIESA 242

Query: 249 IEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRA-AKPRTLNTIGVVG 307
           +  PF +GL+ ER+LF E +D  Q   LIHAFFAERE  K P  R   +PR + ++ VVG
Sbjct: 243 VHLPFSQGLKRERELFNEALDDDQSKALIHAFFAEREAAKIPGFRTDVRPREIKSVAVVG 302

Query: 308 GGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSR 367
            G MG GIA+A  +AG PV +++RD A+L+RG A + K Y+ ++ +GRL        +S 
Sbjct: 303 SGHMGGGIAMAFANAGFPVIVLDRDQAALSRGLAVVAKNYESMVRRGRLDQPGMNKRLSA 362

Query: 368 WSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSV 427
              + +Y  LA  DLV+EA FED+ VK+ VF +LDR CK GA+ A+NTS LDID +AS  
Sbjct: 363 IRSTVNYKDLADVDLVVEAAFEDIGVKEQVFRDLDRACKKGAIFASNTSTLDIDEIASFT 422

Query: 428 SRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGN 487
            RP DVIG HFFSPAN+ +L+EVV  K+ SADV+ATA  +AKK+ K  V  G CDGF GN
Sbjct: 423 RRPGDVIGTHFFSPANVQRLVEVVRGKETSADVLATAMAVAKKIGKIGVAVGNCDGFAGN 482

Query: 488 RVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRN 547
           R+L  Y + A  ++E+GA+P ++D A+  +G  MGPF V DL G D+ W  R+RR     
Sbjct: 483 RMLEKYVTEAMIILEEGATPAEVDTALTRWGLAMGPFAVFDLTGIDVNWHIRQRRLKQGK 542

Query: 548 PAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSF 607
           P      + DR  + G FGQK+G+GFY Y  GSR+  PDPE +AII+A R   G   +S 
Sbjct: 543 PYGS--ALLDRFYDAGRFGQKTGKGFYRYETGSRAPLPDPEADAIIEAYRREVGPRVKSV 600

Query: 608 TDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPK 667
           +++EI++R + A++NEGAN++ E +  R  D+D  ++ GYGFP +RGGPMKYA++ GL +
Sbjct: 601 SEQEIVKRTIYALVNEGANILDEGVVYRSGDIDTIYINGYGFPAWRGGPMKYAELRGLAE 660

Query: 668 ILADIREFAKEDPLFWKPSPLLIELV 693
           +L+D+  F       W+P+ LL  LV
Sbjct: 661 VLSDLDIFHMRFGDRWRPAALLKSLV 686


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: 1097
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: 695
Length adjustment: 39
Effective length of query: 667
Effective length of database: 656
Effective search space:   437552
Effective search space used:   437552
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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Protein sequences (fasta format)
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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