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:

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