Alignments for a candidate for paaH in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Dinoroseobacter shibae DFL-12

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate 3610445 Dshi_3826 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)

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



>FitnessBrowser__Dino:3610445
          Length = 673

 Score =  506 bits (1302), Expect = e-147
 Identities = 294/663 (44%), Positives = 387/663 (58%), Gaps = 14/663 (2%)

Query: 21  VTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPPVPP 80
           VT+D+ PVNA S  VR+GLL A+      +     ++  AGR FIAG D+REF  PP PP
Sbjct: 18  VTVDNPPVNATSTAVRQGLLDAVTRV---QGARLAILRCAGRTFIAGGDMREFDAPPQPP 74

Query: 81  SLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGLLPGAG 140
            LPDV + IEA   P VA + G  LGGGLE+A+   YRIA  G + GLPEV +GL+PGAG
Sbjct: 75  DLPDVVDAIEASATPFVAVMQGTVLGGGLEIAMGCAYRIAAPGTRFGLPEVTVGLIPGAG 134

Query: 141 GTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHELLAAHA 200
           GTQR PRL G  AA+D+  +G+  SA+EA A G +D +    +  A  L     +  +  
Sbjct: 135 GTQRAPRLFGWDAAIDMACAGKLLSAQEAHARGALDAIADDPEAAARALVPEPRIPVSER 194

Query: 201 PVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDEGLRVE 260
           P     D+A ++    +LAA          ++RG  +PL+ +DA+  A   PF EG R E
Sbjct: 195 PAPPPPDSARIAAHRRTLAA----------RARGQTAPLQALDALLWATG-PFREGQRKE 243

Query: 261 RKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIGVVGGGTMGAGIAVAVL 320
           R L L    S Q   L HAFFAER V +    R   PR +  I V+GGG MGAGIA A L
Sbjct: 244 RALHLSLRASDQSRALRHAFFAERTVARPAVIRDRTPREIARIAVMGGGLMGAGIAAACL 303

Query: 321 DAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSYDALAGA 380
            AG  V ++ERD A+    R  +  +  G + +G++   +  A  +           A A
Sbjct: 304 GAGYRVDLLERDAATAEAARDRVRGLIAGALRRGKIDQARHDAHCAALRTGVGIGHAAEA 363

Query: 381 DLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVIGLHFFS 440
           DL IEAVFE+ A K+A FA L +V    A+LATNTSYLD   + + +  P   +GLHFF+
Sbjct: 364 DLAIEAVFEETATKRAAFAALAQVMAPDAILATNTSYLDPREIFAGIPAPDRCLGLHFFA 423

Query: 441 PANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYRSAADAM 500
           PA++MKLLEVV   + SA+ +ATAF LA +LRK  V +G+CDGFIGNR+LA YR AA+ M
Sbjct: 424 PAHVMKLLEVVRLPETSAETLATAFALAGRLRKVAVLSGICDGFIGNRMLAAYRRAAEYM 483

Query: 501 MEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQIADRLC 560
           + DGA P QID A+RA+G  MGPF+  DL+G  I  A R+R+ ATR    RYV ++D+LC
Sbjct: 484 LADGALPEQIDGAMRAYGMAMGPFEAQDLSGLHIAEANRRRQDATRPARERYVTLSDQLC 543

Query: 561 ERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIRRYMAAM 620
             G  GQ++G+G+Y Y EG R    DP V A+I    A  G+  R+    EI  R +A +
Sbjct: 544 ALGRTGQRAGKGWYAYAEGDRRPRVDPAVTALITDYSAAHGLPRRTHDAGEIQARLLAVL 603

Query: 621 INEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIREFAKEDP 680
            NEGA +V E IA     VD+  L+GYGFPR+RGGP+  A   G   I A +       P
Sbjct: 604 ANEGARLVEEGIADSDAAVDMVKLHGYGFPRWRGGPLFAARQAGDATIRAALDALDAASP 663

Query: 681 LFW 683
             W
Sbjct: 664 GSW 666


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: 1146
Number of extensions: 49
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: 673
Length adjustment: 39
Effective length of query: 667
Effective length of database: 634
Effective search space:   422878
Effective search space used:   422878
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, or view the source code.

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