GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3033 in Magnetospirillum magneticum AMB-1

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate WP_011386479.1 AMB_RS20890 iron-sulfur cluster-binding protein

Query= uniprot:Q726S3
         (717 letters)



>NCBI__GCF_000009985.1:WP_011386479.1
          Length = 478

 Score =  272 bits (696), Expect = 2e-77
 Identities = 175/452 (38%), Positives = 234/452 (51%), Gaps = 21/452 (4%)

Query: 24  RNAMDKFAVAYRASRANAFKDIDE-KAIIAEVADAKDHAAKNMDTLYAQFKAEAEKRGVK 82
           R AMD         RA  F D  E  A+ A  A A+ +A   +  L  Q +A   + G+ 
Sbjct: 28  RRAMD----GLMTKRAAQFADEAEWNALRARGAAARANALAKLPELLEQLEANCLRNGIH 83

Query: 83  VHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWII 142
           VH A T AEAN I+  I      +  IK KSM  EE HLN  LE+  +  +E+DLGE+II
Sbjct: 84  VHWAETTAEANAIVLGILEAAGARTVIKGKSMVTEEMHLNAHLEKHGITPVESDLGEYII 143

Query: 143 QMRHEGPSHMVMPAIHLSRYQVADLFSE-VTKQKQEVDIQRLVKVARRELRTHFATADMG 201
           Q+  E PSH+VMP IH ++ ++A+LF + +  Q    ++  L   AR  LR  FA AD G
Sbjct: 144 QLAGEAPSHIVMPCIHKNKTEIAELFHDKIEGQPYTENVDELTAAARAALRGAFAGADAG 203

Query: 202 ISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNA 261
           ISG NFAVAETGT+ L+ NEGN RL TTLP +H+A+ G++K++  L D    L +LPR+A
Sbjct: 204 ISGVNFAVAETGTLVLIENEGNGRLSTTLPPLHIAVTGIEKVLEKLDDVPPLLSLLPRSA 263

Query: 262 TGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPLFSQVLRCVRCGACAN 321
           TGQ IT+YV  I    + E   DG K +H+V LDNGR  +  D      LRC+RC AC N
Sbjct: 264 TGQPITTYVNMISSPRK-EGEKDGPKAVHLVLLDNGRSRVHGDTELRDTLRCIRCAACMN 322

Query: 322 VCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCESCKHICAGGIDLPR 381
            CPVY  VGGH     Y G IG +LT    G D A +       C +C  +C   I +P 
Sbjct: 323 HCPVYTRVGGHTYTFTYPGPIGKLLTPQIEGLDCAGDQPHASTLCRACADVCPVQIPIPD 382

Query: 382 LIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFAKWAQKPVTGGTPYIRHLPQIF 441
           L+     RL  E   P +    G+ +K      T      W    +   +P +    +I 
Sbjct: 383 LL----VRLRTESVRPTQ----GQAVKGAGSSATTSETLGWKGWTLLYASPLVY---RIG 431

Query: 442 AKDHGFKALPAIADKPFRDEWETVRPRIAKPK 473
            K  G+      +  P   +W +VR    KPK
Sbjct: 432 TKMLGWFGNLMPSSAPMLKQWTSVR---TKPK 460


Lambda     K      H
   0.321    0.135    0.402 

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: 767
Number of extensions: 42
Number of successful extensions: 4
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: 717
Length of database: 478
Length adjustment: 37
Effective length of query: 680
Effective length of database: 441
Effective search space:   299880
Effective search space used:   299880
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 (21.9 bits)
S2: 53 (25.0 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