Aligments for a candidate for fadB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for fadB in Cupriavidus basilensis 4G11

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate RR42_RS10265 RR42_RS10265 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS10265
          Length = 692

 Score =  583 bits (1504), Expect = e-171
 Identities = 311/685 (45%), Positives = 430/685 (62%), Gaps = 8/685 (1%)

Query: 18  VLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPP 77
           V +++I + PVN L  DVR G++  I+ A AD  V A+++ GAG+ F  GAD+REF  P 
Sbjct: 11  VAVISIANPPVNGLGYDVRVGIIDGIDRAAADDNVRAIVLTGAGKAFSGGADMREFNSPE 70

Query: 78  V--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGL 135
               P L  V   IE   K VVAA+H  A+GGGLE+ALA HYR+AV  A++ L EV +GL
Sbjct: 71  AWREPGLNTVLVAIENSIKLVVAAVHSVAMGGGLELALACHYRVAVPKARIALSEVTMGL 130

Query: 136 LPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHEL 195
           LPGAGGTQR PRLIG +AA ++I+ G    ++     GL DRL   D + A  +A+  E+
Sbjct: 131 LPGAGGTQRLPRLIGLEAATNMIVHGTSIPSEALADTGLFDRLVEGDVVTA-AVAFAQEV 189

Query: 196 LAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDE 255
            A   P  R RD            AVA  R   A + + L +PL+ +DA+EA+ + PFDE
Sbjct: 190 AARPGPHPRVRDLTIRHPTPEGYLAVA--RPAVAARYKNLQAPLRCLDAIEASFKLPFDE 247

Query: 256 GLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGVVGGGTMGAG 314
           GL +ER+LFLE ++ P    L HAFF+ER   K  +   + P R +N + VVG G MG+G
Sbjct: 248 GLALERRLFLELMNGPVSKSLRHAFFSERAAAKLADVPDSVPERAVNKVAVVGAGLMGSG 307

Query: 315 IAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSY 374
           IA+  L AG+PV +++  D  + +G A I + Y+  + KG+L AE   A M+    +   
Sbjct: 308 IAMNFLSAGIPVVLLDISDEVVQKGAAAIRRNYEASLKKGKLRAEVVEARMALLQPTVDL 367

Query: 375 DALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVI 434
             +A  DLVIEA++ED+ VK  +F  LD + + GA+LATNTS LD+D +A+   RP DV+
Sbjct: 368 GRVAACDLVIEAIYEDMDVKLRMFRALDEIARPGAILATNTSMLDVDRIAAETRRPQDVV 427

Query: 435 GLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYR 494
           GLHFFSPAN+M+LLEVV   + + DV+ TA  LA+++ K PV +GVCDGFIGNR+LA Y 
Sbjct: 428 GLHFFSPANVMRLLEVVRGAKTAPDVLQTAMRLARRIGKVPVVSGVCDGFIGNRMLAKYT 487

Query: 495 SAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQ 554
             A  ++E GA P Q+D A+  FG  MGPF++ DLAG DIGWA RKR  A  +P+    +
Sbjct: 488 RRAGELLEQGAFPEQVDRAIEEFGLAMGPFRMADLAGNDIGWAIRKRHYA-EDPSQPRFE 546

Query: 555 IADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIR 614
           + DRLCE G FGQK+G G+Y Y  G R   P     A+++A     G+ PR F+ +EI+ 
Sbjct: 547 LGDRLCEAGHFGQKTGTGWYDYEAGQRKALPSARTRAMLEAYWKERGVVPRRFSGQEIVE 606

Query: 615 RYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIRE 674
           R + A++NEGA V+ E IA R  D+D  +L+GYGFP +RGGPM YAD VG+  +   +R 
Sbjct: 607 RLIYALVNEGAAVLDEGIAARASDIDAVYLHGYGFPAWRGGPMFYADTVGVTNVRRTLRA 666

Query: 675 FAKEDPLFWKPSPLLIELVERGADF 699
            + +DP  WKP+ L+ +L ++G  F
Sbjct: 667 LSAKDP-SWKPAALIEQLADKGRTF 690


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: 1063
Number of extensions: 49
Number of successful extensions: 5
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: 692
Length adjustment: 39
Effective length of query: 667
Effective length of database: 653
Effective search space:   435551
Effective search space used:   435551
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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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, 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