GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Shewanella amazonensis SB2B

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 6938573 Sama_2676 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= curated2:Q87L22
         (485 letters)



>FitnessBrowser__SB2B:6938573
          Length = 1058

 Score =  193 bits (491), Expect = 2e-53
 Identities = 155/471 (32%), Positives = 229/471 (48%), Gaps = 37/471 (7%)

Query: 2    THWIAGEWVQGQ---GEEFVSLSPYNQEV-IWRGNGATAEQVDQAVAAARAAFVEWKKRP 57
            T W AG  V G+   GE    +SPYN  + + +   A    ++QA+A A  AF  W + P
Sbjct: 561  TQWSAGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTP 620

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

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

Query: 168  KPSEQTPWTGELAMKLWEEAGLPKGVINLVQG-AKETGIALADAKGIDGILFTGSANTGH 226
            KP+EQT   G  A++L  EAG+PK V+  + G     G  L   + I G+ FTGS  T  
Sbjct: 733  KPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAK 792

Query: 227  ILHRQFAGQPGKMLAL--EMGGNNPMVISDNYGDLDATVYTIIQSAFISAGQRCTCARRL 284
            +++R  AG+ G ++ L  E GG N MV+ D+    +  V  ++ SAF SAGQRC+  R L
Sbjct: 793  VINRALAGRDGAIIPLIAETGGQNAMVV-DSTSQPEQVVNDVVSSAFTSAGQRCSALRVL 851

Query: 285  YVPFGEKGDALITKLVEATKNIRMDQPFAEPAPFMGPQISVAAAKFILDAQANLQSLGGE 344
            Y+   +  + ++  L  A   + +  P +     +GP I  AAAK  L+A  +     G 
Sbjct: 852  YLQ-EDIAERVLDVLKGAMDELTLGNPGSVKTD-VGPVID-AAAKANLNAHIDHIKQVGR 908

Query: 345  SLIEAKAGEAA----FVSPGIIDVTNIAELPDEEYFGPLLQVVRYE--GLDKAVELANDT 398
             + +    E      FV+P  +++ +I  L  +E FGP+L VVRY+  GL K ++  N T
Sbjct: 909  LIHQLSLPEGTENGHFVAPTAVEIDSIKVL-TKENFGPILHVVRYKAAGLQKVIDDINST 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: 1097
Number of extensions: 60
Number of successful extensions: 7
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: 1058
Length adjustment: 39
Effective length of query: 446
Effective length of database: 1019
Effective search space:   454474
Effective search space used:   454474
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:

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