GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Magnetospirillum magneticum AMB-1

Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_011386311.1 AMB_RS20025 malate dehydrogenase

Query= BRENDA::Q27797
         (326 letters)



>NCBI__GCF_000009985.1:WP_011386311.1
          Length = 319

 Score =  313 bits (803), Expect = 3e-90
 Identities = 162/315 (51%), Positives = 216/315 (68%), Gaps = 7/315 (2%)

Query: 8   RKKIAMIGSGMIGGTMGYLCVLRELADVVLFDVVTGMPEGKALDDSQATSIADTNVSVTS 67
           RKKIA++GSG IGGT+ +L  L+EL DVV+FD+  G+P+GK LD  ++T +   +   + 
Sbjct: 3   RKKIALVGSGNIGGTLAHLIGLKELGDVVMFDIAEGIPQGKGLDILESTPVEGVDCRYSG 62

Query: 68  ANQYEKIAGSDVVIITAGLTKVPGKSDKEWSRNDLLPFNAKIIREVAQGVKKYCPLAFVI 127
           AN Y  IAG+DVVI+TAG+ + PG S     R+DL+  N K++  V +G+KK CP AFVI
Sbjct: 63  ANDYSAIAGADVVIVTAGVPRKPGMS-----RDDLVGINLKVMAAVGEGIKKNCPGAFVI 117

Query: 128 VVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTHG 187
            +TNPLD MV      SG+P NM+ GMA VLDSARFR F+ ++  +S  D+ A V+G HG
Sbjct: 118 CITNPLDVMVWALQHYSGVPANMIVGMAGVLDSARFRTFLCEEFNVSVEDVTAFVLGGHG 177

Query: 188 DHMLPLARYVTVSGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYYAPAL 247
           D M+PL RY TV+G PL + +K G  T+ KL +IV+RT+  G EIV LL  GSAYYAPA 
Sbjct: 178 DTMVPLVRYSTVAGIPLPDLVKMGWTTQEKLDQIVQRTRDGGAEIVNLLKTGSAYYAPAA 237

Query: 248 SAITMAQAFLKDEKRVLPCSVYCQ-GEYGL-HDMFIGLPAVIGGGGIEQVIELELTHEEQ 305
           S + MA+AFLKD+KRVLP +   + G YG   D+F+G+P VIG GG+E+++E+EL   EQ
Sbjct: 238 SGVAMAEAFLKDKKRVLPVATLVKGGTYGQPDDVFVGVPVVIGEGGVERIVEIELNAAEQ 297

Query: 306 ECFRKSVDDVVELNK 320
             F KS D V  L K
Sbjct: 298 AEFNKSADAVRGLVK 312


Lambda     K      H
   0.320    0.137    0.395 

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: 283
Number of extensions: 12
Number of successful extensions: 3
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: 326
Length of database: 319
Length adjustment: 28
Effective length of query: 298
Effective length of database: 291
Effective search space:    86718
Effective search space used:    86718
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: 48 (23.1 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