GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Shewanella amazonensis SB2B

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate 6939201 Sama_3295 methylcitrate synthase (RefSeq)

Query= SwissProt::Q8EJW2
         (375 letters)



>FitnessBrowser__SB2B:6939201
          Length = 378

 Score =  674 bits (1738), Expect = 0.0
 Identities = 327/371 (88%), Positives = 348/371 (93%)

Query: 5   KKLTGAGLRGQSAGETALSTVGVSGSGLTYRGYDVKDLAENATFEEVAYLILYGELPTTA 64
           KKL+GAGLRGQSAGETALSTVG SGSGLTYRGYDVKDLAENA+FEEVA+LILYGELPT  
Sbjct: 7   KKLSGAGLRGQSAGETALSTVGKSGSGLTYRGYDVKDLAENASFEEVAFLILYGELPTQL 66

Query: 65  QLAAYKTKLKGMRGLPQALKEVLERIPADAHPMDVMRTGCSMLGNLEAEHSFSEQSQIAD 124
           +L  Y+ KLKG+RGLPQALKEVLERIPA+AHPMDV+RTGCSMLGNLE EHSF++Q  + +
Sbjct: 67  ELDNYRAKLKGLRGLPQALKEVLERIPANAHPMDVLRTGCSMLGNLETEHSFADQFDVTN 126

Query: 125 RLLAAFPSIICYWYRFSHDGVRIDTETDDDQIGAHFLHLLHGKAPSALHTKVMDVSLILY 184
           R+LA FPSIICYWYRFSHDGVRI+TETDD+QIGAHFLHLLHGKAPSALH +VMDVSLILY
Sbjct: 127 RMLAVFPSIICYWYRFSHDGVRIETETDDEQIGAHFLHLLHGKAPSALHARVMDVSLILY 186

Query: 185 AEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDMKDEADARD 244
           AEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDM+DE  ARD
Sbjct: 187 AEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDMRDEQHARD 246

Query: 245 VLMGKLERKEKIMGFGHAIYRDSDPRNAIIKEWSEKLAADYGDDRLYRVSVACEALMWEQ 304
           VL G LERKEKIMGFGHAIYR+SDPRNAIIKEWSEKLA +YGDDRLYRVSVACEA MWEQ
Sbjct: 247 VLAGMLERKEKIMGFGHAIYRESDPRNAIIKEWSEKLAKEYGDDRLYRVSVACEAFMWEQ 306

Query: 305 KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRVTGWTAHVMEQRSNNRIIRPSADYVGV 364
           KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRV+GWTAHVMEQRSNNRIIRPSADYVGV
Sbjct: 307 KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRVSGWTAHVMEQRSNNRIIRPSADYVGV 366

Query: 365 SPRKVIPIANR 375
             R V PI+ R
Sbjct: 367 ELRSVTPISER 377


Lambda     K      H
   0.320    0.134    0.401 

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: 573
Number of extensions: 13
Number of successful extensions: 1
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: 375
Length of database: 378
Length adjustment: 30
Effective length of query: 345
Effective length of database: 348
Effective search space:   120060
Effective search space used:   120060
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: 50 (23.9 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