Alignments for a candidate for fadB in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Sphingomonas koreensis DSMZ 15582

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate Ga0059261_2827 Ga0059261_2827 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Korea:Ga0059261_2827
          Length = 683

 Score =  540 bits (1390), Expect = e-157
 Identities = 309/689 (44%), Positives = 418/689 (60%), Gaps = 29/689 (4%)

Query: 18  VLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPP 77
           V +VT+D  PVNA+S  +  GL  A+ AA +D A +A++++ AGR FIAGAD++  GK  
Sbjct: 16  VAIVTLDFPPVNAMSPALMDGLYDALMAALSDDAAKAIVLICAGRTFIAGADLKSLGKVQ 75

Query: 78  VPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGLLP 137
                  + + IE   KP VAA+HG ALGGG+E AL  HYRIAV  A++GLPEV LGLLP
Sbjct: 76  PKVDFFALQDSIENSPKPTVAALHGTALGGGMETALTFHYRIAVPSARMGLPEVNLGLLP 135

Query: 138 GAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHELLA 197
           G GGTQR PR+ GA+AALDL++SGR   AKEAL  GLIDRL +   +  + +A+  EL+ 
Sbjct: 136 GGGGTQRLPRITGAEAALDLLISGRQVGAKEALTIGLIDRLAAEGALREDAIAFAKELVD 195

Query: 198 AHAPVRRTRDAAA--LSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDE 255
           A  P +R RD  A   +DR  +       R   AK+  GL +P  IV  VEAA+  P+++
Sbjct: 196 AGEPPKRIRDCEAKVAADRKDA-NLFERFRTSHAKQLNGLDAPQAIVRCVEAAVAGPWEK 254

Query: 256 GLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRT-LNTIGVVGGGTMGAG 314
           GL +ER  F   +  PQ A L H F AER   K P  RA  P   +  +G+VG GTMG+G
Sbjct: 255 GLAIERTEFQTLLAGPQSAALRHVFMAERAAQKIPGLRADLPLIPVTKVGIVGAGTMGSG 314

Query: 315 IAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSY 374
           IA+A L AG  VT++E   A+L RG AHI       + +G+L+A+K  A ++  + +   
Sbjct: 315 IAMAFLAAGFAVTVVETQQAALDRGVAHITATLQSRVERGKLAADKAEAQIAALTPTLDL 374

Query: 375 DALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVI 434
            ALA ADLV+EA+FE+LA KQA+F  L  + +   +LATNTS+LD+DA+A+  + P  V+
Sbjct: 375 SALADADLVVEAIFENLAAKQALFGTLSAIVRPDTILATNTSFLDVDAIAAGAAGPERVL 434

Query: 435 GLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYR 494
           G+HFFSPAN+M+LLEVV   + S  V+A+   LAKKL K  V +GVC GFIGNR+LA  +
Sbjct: 435 GMHFFSPANVMRLLEVVRAAKTSEAVLASVMALAKKLGKAAVVSGVCFGFIGNRMLAARQ 494

Query: 495 SAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQ 554
             ADAM+  G  P+ ID  +  FGFPMGPF ++DLAG DIGW                  
Sbjct: 495 VHADAMVLAGVLPWNIDRILTGFGFPMGPFAMLDLAGLDIGWEGDTD------------S 542

Query: 555 IADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFT--DEEI 612
           +  RL   G  GQKSG G+Y Y     + TP P  +  +D     A + P S T  D EI
Sbjct: 543 VKSRLVAAGRKGQKSGAGYYDY----ENKTPSPS-QTALDVIAGLASVAPGSVTLSDREI 597

Query: 613 IRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADI 672
           + R +  MINEGA ++ E IALR  D+D+ ++ GYG+P   GGPM +AD +GL +++  +
Sbjct: 598 LDRLLLPMINEGAKILEEGIALRGSDIDLVWITGYGWPAQTGGPMFHADAIGLTRVVDGL 657

Query: 673 REFAKEDPLFWKPSPLLIELVERGADFAS 701
           R    E      P+ LL++L   G   A+
Sbjct: 658 RHMGVE------PAALLLKLASEGGSLAA 680


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: 1082
Number of extensions: 45
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: 683
Length adjustment: 39
Effective length of query: 667
Effective length of database: 644
Effective search space:   429548
Effective search space used:   429548
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
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