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

GapMind for catabolism of small carbon sources

Aligments 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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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