GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Shewanella oneidensis MR-1

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 202865 SO3774 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, putative (NCBI ptt file)

Query= curated2:Q87L22
         (485 letters)



>lcl|FitnessBrowser__MR1:202865 SO3774 proline
            dehydrogenase/delta-1-pyrroline-5-carboxylate
            dehydrogenase, putative (NCBI ptt file)
          Length = 1059

 Score =  190 bits (483), Expect = 2e-52
 Identities = 153/471 (32%), Positives = 234/471 (49%), Gaps = 37/471 (7%)

Query: 2    THWIAGEWVQGQ---GEEFVSLSPYNQ-EVIWRGNGATAEQVDQAVAAARAAFVEWKKRP 57
            T W AG  V GQ   GE    +SP++  + + +   A    ++QAV++A AAF  W + P
Sbjct: 561  TQWQAGPLVNGQPLTGEHKTIVSPFDTTQTVGQVAFADKAAIEQAVSSAHAAFGSWTRTP 620

Query: 58   FAEREAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEA----------AAMAGKIAI 107
               R + +   A+ ++EN E++  +  +E GK I +   E           A  A K+  
Sbjct: 621  VEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMS 680

Query: 108  SIRAYHDRTGEATREAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVF 167
                    TGE       N++ L+ R  GV     P+NFP  +  G +  AL AGNTVV 
Sbjct: 681  KPELLPGPTGEL------NELFLQGR--GVFVCISPWNFPLAIFLGQVSAALAAGNTVVA 732

Query: 168  KPSEQTPWTGELAMKLWEEAGLPKGVINLVQGAKET-GIALADAKGIDGILFTGSANTGH 226
            KP+EQT   G  A++L  +AG+P  V+  + G   T G AL   + I G+ FTGS  T  
Sbjct: 733  KPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAK 792

Query: 227  ILHRQFAGQPGKMLAL--EMGGNNPMVISDNYGDLDATVYTIIQSAFISAGQRCTCARRL 284
            +++R  A + G ++ L  E GG N MV+ D+    +  V  ++ S+F SAGQRC+  R L
Sbjct: 793  LINRTLANREGAIIPLIAETGGQNAMVV-DSTSQPEQVVNDVVSSSFTSAGQRCSALRVL 851

Query: 285  YVPFGEKGDALITKLVEATKNIRMDQPFAEPAPFMGPQISVAAAKFILDAQAN----LQS 340
            ++   +  D +I  L  A   + +  P +     +GP I  A AK  LDA  +    +  
Sbjct: 852  FLQ-EDIADRVIDVLQGAMDELVIGNPSSIKTD-VGPVID-ATAKANLDAHIDHIKQVGK 908

Query: 341  LGGESLIEAKAGEAAFVSPGIIDVTNIAELPDEEYFGPLLQVVRYEGLDKA--VELANDT 398
            L  +  + A      FV+P  +++ +I  L ++E+FGP+L V+RY+  + A  ++  N T
Sbjct: 909  LIKQMSLPAGTENGHFVAPTAVEIDSIKVL-EKEHFGPILHVIRYKASELAHVIDEINST 967

Query: 399  RFGLSAGLVSTDDQEWEYFVDHIRAGIVNRNRQLTGA-SGDAPFGGPGASG 448
             FGL+ G+ S ++       D +  G V  NR   GA  G  PFGG G SG
Sbjct: 968  GFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSG 1018


Lambda     K      H
   0.316    0.134    0.397 

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: 1110
Number of extensions: 55
Number of successful extensions: 6
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: 485
Length of database: 1059
Length adjustment: 39
Effective length of query: 446
Effective length of database: 1020
Effective search space:   454920
Effective search space used:   454920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 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