Alignments for a candidate for fadB in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Sulfuritalea hydrogenivorans DSM 22779

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_041097743.1 SUTH_RS05635 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

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



>NCBI__GCF_000828635.1:WP_041097743.1
          Length = 697

 Score =  632 bits (1630), Expect = 0.0
 Identities = 325/690 (47%), Positives = 459/690 (66%), Gaps = 9/690 (1%)

Query: 13  ELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIRE 72
           +L G   ++T+D+ PVN L  D+R G++A I+ A AD AV+AV+++G+ R F  GADIRE
Sbjct: 7   QLHGSTAVITLDNPPVNGLGYDLRCGIVAGIDQATADPAVKAVVLIGSDRAFSGGADIRE 66

Query: 73  FGKPP--VPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPE 130
           FG P     P+L  V   +EAC KPVVAAI G  +GGGLE+ L  H+R+A+ GA + LPE
Sbjct: 67  FGSPKSYAEPNLLTVIRIVEACPKPVVAAIGGVCMGGGLELTLGCHFRVAIAGASIALPE 126

Query: 131 VQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRL--GSSDDILAEG 188
           ++LGLLPGAGGTQR PR++G +AAL+LILSG    +++     L D    G+  D+L   
Sbjct: 127 IKLGLLPGAGGTQRMPRIVGVEAALNLILSGNPVPSEKFKGTPLFDEFIEGNGGDLLKGA 186

Query: 189 LAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAA 248
           LA+  +++A   P++R RD     D     A    +R      +    +P K +DAV+AA
Sbjct: 187 LAFADKVVAEKRPLKRIRDIRI--DYPGQEAFFQFSRNMVKGVAGPFPAPFKCIDAVQAA 244

Query: 249 IEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGVVG 307
           + +PFDEG++ ER  F+E + +P+   L HAF  ER   K P+     P R +  +GV+G
Sbjct: 245 LTKPFDEGMKFERACFIELMGTPESRALRHAFTGERAASKIPDVPDDTPARKIARVGVIG 304

Query: 308 GGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSR 367
            GTMG GI +  L+AG+PVTM+E    +L +G A I K Y+  + KG+L+ EK    M  
Sbjct: 305 AGTMGGGITMNFLNAGIPVTMLEMKQEALDKGIATIRKNYENSMKKGKLTQEKLDQRMGM 364

Query: 368 WSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSV 427
            SG+ SYD    ADL+IEAVFE+++VK+AVF +LD + K GA+LA+NTS LD++ +A+  
Sbjct: 365 LSGTLSYDDFKDADLIIEAVFEEISVKEAVFKQLDAIAKPGAILASNTSTLDVNKIANFT 424

Query: 428 SRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGN 487
            RP DV+G+HFFSPAN+MKLLEVV     + DV+AT  ++AKK++KT V +GVCDGFIGN
Sbjct: 425 KRPQDVVGMHFFSPANVMKLLEVVRGAATAKDVMATVMQVAKKIKKTAVVSGVCDGFIGN 484

Query: 488 RVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRN 547
           R++  Y   A  ++E+GA+P Q+D A+  +G  MGPF++ DLAG DIGWA RKRR   + 
Sbjct: 485 RMIEHYGRVAGFLLEEGATPAQVDKALEKWGMAMGPFRMGDLAGNDIGWAIRKRRYVEK- 543

Query: 548 PAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSF 607
           P+ RY + AD+LCE+G +GQK+G+G+YLY  G+R   PDPEV+ +++A R   GITPR  
Sbjct: 544 PSIRYAKFADKLCEQGRYGQKTGKGWYLYQPGNRKAIPDPEVDTMLEAYRKELGITPRKI 603

Query: 608 TDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPK 667
           +D EI++R + A++NEGA ++ E IA R  D+D+ +L GYGFP +RGGPM YAD VGL  
Sbjct: 604 SDAEIVQRCIYALVNEGARILEEGIAARASDIDMIYLTGYGFPLHRGGPMLYADEVGLYN 663

Query: 668 ILADIREF-AKEDPLFWKPSPLLIELVERG 696
           +   ++EF A     FW+P+PL+ + V  G
Sbjct: 664 VARSMKEFAATSGDAFWEPAPLIAKRVADG 693


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: 1106
Number of extensions: 48
Number of successful extensions: 8
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: 697
Length adjustment: 39
Effective length of query: 667
Effective length of database: 658
Effective search space:   438886
Effective search space used:   438886
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 Apr 09 2024. 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