GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Magnetospirillum magneticum AMB-1

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_011385366.1 AMB_RS15050 multifunctional fatty acid oxidation complex subunit alpha

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



>NCBI__GCF_000009985.1:WP_011385366.1
          Length = 703

 Score =  568 bits (1463), Expect = e-166
 Identities = 317/701 (45%), Positives = 430/701 (61%), Gaps = 4/701 (0%)

Query: 7   ADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIA 66
           +DVV+  +  ++  VTID  PVNA    VR GL        A    +AVL++ AGR F+A
Sbjct: 2   SDVVTLSVSDRIATVTIDSPPVNAADHPVRAGLQKVFTDLAARSDYDAVLVLCAGRTFMA 61

Query: 67  GADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKL 126
           GADI EF      P   D+ N +E C KPVVAA+HG ALG G E+A+A HYRIA  GA++
Sbjct: 62  GADIGEFDTGIKAPHHQDLFNLVENCAKPVVAALHGTALGAGTELAMACHYRIADKGARI 121

Query: 127 GLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILA 186
           GLPE+ LG++PGAGGTQR PRLIG  AA+DL+LSG+   A +A   GL+D + S D + A
Sbjct: 122 GLPELSLGIIPGAGGTQRAPRLIGLDAAMDLVLSGKPLPAPKAAELGLVDEIASGD-LNA 180

Query: 187 EGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVE 246
             LA+  +L+A    VRRT D A   D A     +A  +A+ AK  +   SPLK ++A+ 
Sbjct: 181 AALAFAKKLVAEGKGVRRTCDMAP-KDAAKDAEIIAARQAQVAKTMKNRTSPLKALEAMA 239

Query: 247 AAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPE-TRAAKPRTLNTIGV 305
           A     F EGLR+E  +  +   + +   + H FFA+REV K P  T+  K R +  +G+
Sbjct: 240 ATTTLSFAEGLRLEADISKQLEHAVEARAMRHLFFADREVRKIPGITKDIKARPIRKVGI 299

Query: 306 VGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALM 365
           +G GTMG GIA+   + G+PVT+I+  D +L RG   I K Y+  +++G L+ E+  + M
Sbjct: 300 IGAGTMGGGIAMCFANIGIPVTIIDVSDENLQRGLGVIRKNYERSVSRGSLTQEQLESRM 359

Query: 366 SRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALAS 425
              S ST Y AL  ADL IEAVFE + +K+ +FA+LD V  AGA+L TNTS LDID +A+
Sbjct: 360 GLLSASTDYAALKDADLAIEAVFEKMELKKDIFAKLDAVLPAGAILGTNTSTLDIDEIAN 419

Query: 426 SVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFI 485
           +  RPADVIGLHFFSPAN+M LLE+V  KQ + DV+ TA ++AK ++KT V + VC GFI
Sbjct: 420 TTKRPADVIGLHFFSPANVMPLLEIVQGKQTAMDVLLTALDMAKLIKKTGVVSKVCYGFI 479

Query: 486 GNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAAT 545
           GNR++  Y   A+ M+ +GA+P +ID A+  +G  MG   V D+AG ++G   R      
Sbjct: 480 GNRMMDPYGREAERMVLEGATPAEIDGALEGWGMAMGILAVYDMAGVEVGDNTRIANPHM 539

Query: 546 RNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPR 605
                 + + +  L    W GQK GRG+Y Y    R    DPEV  ++ AE  R  +  R
Sbjct: 540 VPDDPSFYRCSTLLVANKWLGQKVGRGYYRYDSPDRKRASDPEVIEMMHAEGKRLNVPAR 599

Query: 606 SFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGL 665
               +EI+ R + +MINEGA ++ E IALR  D+DV +  GYGFPRYRGGPM YAD +GL
Sbjct: 600 KPGKDEILERCLYSMINEGAKLLEEGIALRASDIDVVYTAGYGFPRYRGGPMFYADTIGL 659

Query: 666 PKILADIREFAKE-DPLFWKPSPLLIELVERGADFASLNQS 705
             I   I EF K  DP +W P+PLL +L + G+ FA  + S
Sbjct: 660 KVIYDKIVEFQKTLDPRYWTPAPLLEKLAKAGSTFAQWDAS 700


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: 1141
Number of extensions: 46
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: 703
Length adjustment: 39
Effective length of query: 667
Effective length of database: 664
Effective search space:   442888
Effective search space used:   442888
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