GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH 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.

Links

Downloads

Related tools

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