GapMind for catabolism of small carbon sources

 

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

Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate WP_011386479.1 AMB_RS20890 iron-sulfur cluster-binding protein

Query= uniprot:Q8EGS5
         (464 letters)



>NCBI__GCF_000009985.1:WP_011386479.1
          Length = 478

 Score =  291 bits (744), Expect = 4e-83
 Identities = 163/406 (40%), Positives = 232/406 (57%), Gaps = 17/406 (4%)

Query: 1   MAYQHNHEAMGSQVHAYKADIFCRDETRVDWHSKALWLLREKRDRAAGSLPEWEQLRQLG 60
           MA + +    G++ H    D   R   R     +A+  L  KR        EW  LR  G
Sbjct: 1   MAAEASKMEFGAKAHVALNDPKLRANFR-----RAMDGLMTKRAAQFADEAEWNALRARG 55

Query: 61  SEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSM 120
           +  + + L  L + LE  E NCL NGI VHWA+  AE N IV  IL +   + ++K KSM
Sbjct: 56  AAARANALAKLPELLEQLEANCLRNGIHVHWAETTAEANAIVLGILEAAGARTVIKGKSM 115

Query: 121 LTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGT 180
           +TEE HLN +LE+ GI  +++DLGE IIQLA   PSHIV+P IH  K E+ +LFHDK+  
Sbjct: 116 VTEEMHLNAHLEKHGITPVESDLGEYIIQLAGEAPSHIVMPCIHKNKTEIAELFHDKIEG 175

Query: 181 KAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKL 240
           +    +   LT AARA LR  F  ADA ++GVN A+A+ G +V+  NEGN  +   LP L
Sbjct: 176 QPYTENVDELTAAARAALRGAFAGADAGISGVNFAVAETGTLVLIENEGNGRLSTTLPPL 235

Query: 241 QLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGE------MHVIIV 294
            +   GI+KV+  +D    LL  L R+ATGQP+TTY      P+ +GE      +H++++
Sbjct: 236 HIAVTGIEKVLEKLDDVPPLLSLLPRSATGQPITTYVNMISSPRKEGEKDGPKAVHLVLL 295

Query: 295 DNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGATHDNTN 354
           DNGR+ +  D  L ++L+CIRC  C+N CPVY R GG++Y +T PGPIG  +    +  +
Sbjct: 296 DNGRSRVHGDTELRDTLRCIRCAACMNHCPVYTRVGGHTYTFTYPGPIGKLLTPQIEGLD 355

Query: 355 SIA---WACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKLPYGK 397
                  A TLC +C  VCP ++P+  ++    RL+ E+ +   G+
Sbjct: 356 CAGDQPHASTLCRACADVCPVQIPIPDLL---VRLRTESVRPTQGQ 398


Lambda     K      H
   0.320    0.134    0.413 

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: 487
Number of extensions: 21
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: 464
Length of database: 478
Length adjustment: 33
Effective length of query: 431
Effective length of database: 445
Effective search space:   191795
Effective search space used:   191795
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: 51 (24.3 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