GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Shewanella amazonensis SB2B

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 6938547 Sama_2650 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__SB2B:6938547
          Length = 496

 Score =  628 bits (1620), Expect = 0.0
 Identities = 307/496 (61%), Positives = 379/496 (76%), Gaps = 2/496 (0%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M  I H + G+  A + RT  VF P+TGEA  +V LA  + + +AI  AKAAF +W    
Sbjct: 1   MQSITHFVNGQHTAPSARTQTVFEPATGEARAQVSLASTQEVGEAIAVAKAAFESWSQMT 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
           P  RA++LF+FK L+EAN + + +LI+ EHGK ++DA GEL RG+E VE+A   P +LKG
Sbjct: 61  PLNRARILFKFKALVEANMDELAQLITREHGKVLDDAKGELIRGLEVVEFACGIPHLLKG 120

Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180
           E++  VG  +DAW+  QP+GVVAGI PFNFP MVP+WM+P+AIACGNTFI+KPSE+DPSS
Sbjct: 121 EHTAQVGTGVDAWAVNQPLGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSS 180

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
            + IAEL  EAGLP GV NVV+GDK AVD L+   +++A+SFVGSTPIAEYIY+  +  G
Sbjct: 181 VMRIAELLKEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYATASAHG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNH +LMPDADLD AV+ALMGAAYGS GERCMAISV + VGD   DALV+K
Sbjct: 241 KRVQALGGAKNHMLLMPDADLDQAVNALMGAAYGSAGERCMAISVVLAVGD-AGDALVEK 299

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           L+P+I  LK+G G    ++MGPL++    DKV+ Y++ GV +GA L+VDGR   +    N
Sbjct: 300 LLPKIAALKVGNGLIPDMEMGPLISAQHLDKVSSYVEAGVREGASLLVDGRELSMEDKAN 359

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           G+FLG  LFD VTP+M+IYKEEIFGPVL IVRV     A+QLINDHE+GNGT IFT+ GE
Sbjct: 360 GYFLGACLFDHVTPQMSIYKEEIFGPVLSIVRVPDYNSALQLINDHEFGNGTAIFTQSGE 419

Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480
           AAR FC  ++VGMVGVNVP+PVP+A+HSFGGWKRSLFG LH +GPDGVRFYTKRKAIT R
Sbjct: 420 AARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITAR 479

Query: 481 WPQRKSHEAAQFAFPS 496
           WPQ K   AA+F  P+
Sbjct: 480 WPQGK-QLAAEFVMPT 494


Lambda     K      H
   0.319    0.137    0.411 

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: 735
Number of extensions: 25
Number of successful extensions: 2
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: 498
Length of database: 496
Length adjustment: 34
Effective length of query: 464
Effective length of database: 462
Effective search space:   214368
Effective search space used:   214368
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 (21.7 bits)
S2: 52 (24.6 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