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.- (characterized)
to candidate WP_011384977.1 AMB_RS13065 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::P76083
         (475 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384977.1 AMB_RS13065
           3-hydroxyacyl-CoA dehydrogenase
          Length = 506

 Score =  273 bits (699), Expect = 8e-78
 Identities = 173/486 (35%), Positives = 253/486 (52%), Gaps = 24/486 (4%)

Query: 8   VAVIGSGTMGAGIAEVAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGKLTAETCE 67
           + ++GSGTMG GIA++A + G  V+L D    A  +A D + A L     +GKLTAE C 
Sbjct: 12  LGLVGSGTMGRGIAQIAVASGVTVILVDALPGAAAKARDAVSAMLAKLAEKGKLTAEACA 71

Query: 68  RTLKRLIPVTDIHALAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNTSSISITA 127
               RL     +  LA   +V+EA  E ++VK+AL   L  +     L+ +NTSS+S+T+
Sbjct: 72  SATARLKLGESLADLAPCHVVVEAIVEDIKVKQALMKDLEAIVSKDCLIASNTSSLSVTS 131

Query: 128 IAAEIKNPERVAGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQPVRCHSTP 187
           IAA  ++P+RV G HFFNP P+MK+VEV+ G+ TA  VVE L  L    G  PV+   TP
Sbjct: 132 IAAACQHPQRVGGFHFFNPVPLMKVVEVIDGVMTAPWVVETLTALARRMGHTPVKAKDTP 191

Query: 188 GFIVNRVARPYYSEAWRALEEQVAAPEVIDAALRDGAGFPMGPLELTDLIGQDVNFAVTC 247
           GF+VN   R Y +EA + + E V      D  L+  AGF MGP EL DL   DV+  V  
Sbjct: 192 GFVVNHAGRGYGTEALKLVGEGVTDFFTADRILKGAAGFRMGPFELLDLTALDVSHPVME 251

Query: 248 SVFNAFWQERRFLPSLVQQELVIGGRLGKKSGLGVYDWRAEREAVVGLEAVSDSFSPMKV 307
           S+++ ++QE RF PS + +  ++ G LG+K+G G Y +  ++  V     V  ++     
Sbjct: 252 SIYDQYYQEPRFRPSPITRSRLVAGLLGRKTGRGFYAYEGDKAVVPPAPPVPAAWQGPVW 311

Query: 308 EKKSDG-------VTEIDD------------VLLIETQGETAQALAIRL---ARPVVVID 345
               +G       VT++              ++LI   GE      +RL   A   V ID
Sbjct: 312 VAPGEGSLAVAALVTKLGASLETGEKPGETALILIPVLGEDCTTAVVRLGLDAARSVAID 371

Query: 346 KMAG--KVVTIAAAAVNPDSATRKAIYYLQQQGKTVLQIADYPGMLIWRTVAMIINEALD 403
            + G     T+    V        A   L      V  IAD PG++  R VA I+N   D
Sbjct: 372 PLFGLDSHRTVMTNPVTRAEIRDGAHGLLAGDEVAVSVIADSPGLVAQRVVATIVNIGCD 431

Query: 404 ALQKGVASEQDIDTAMRLGVNYPYGPLAWGAQLGWQRILRLLENLQHHYGEERYRPCSLL 463
             Q+ +A+  DID A+ LG+ YP GPL+WG ++G  +++ +L+ +    G+ RYR    L
Sbjct: 432 IAQQRIATPDDIDKAVTLGLGYPAGPLSWGDRIGAAKVVAILDTVLAITGDPRYRASLWL 491

Query: 464 RQRALL 469
           ++RA L
Sbjct: 492 KRRAAL 497


Lambda     K      H
   0.319    0.134    0.386 

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: 554
Number of extensions: 25
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 475
Length of database: 506
Length adjustment: 34
Effective length of query: 441
Effective length of database: 472
Effective search space:   208152
Effective search space used:   208152
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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