GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Azospirillum brasilense Sp245

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 AZOBR_RS22500 AZOBR_RS22500 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS22500 AZOBR_RS22500
           methylmalonate-semialdehyde dehydrogenase
          Length = 499

 Score =  742 bits (1915), Expect = 0.0
 Identities = 357/497 (71%), Positives = 416/497 (83%), Gaps = 1/497 (0%)

Query: 1   MTLIKHLIGGELIADTG-RTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNT 59
           M L+ HLIGG   A    R+AD+ NP+TGE V +VPLA R T++ AI AA+AAFPAWR T
Sbjct: 1   MPLVPHLIGGAADAPAETRSADIVNPATGETVGRVPLAGRATVESAIAAAEAAFPAWRAT 60

Query: 60  PPAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILK 119
           PPAKRA+V+FRF+QLLE N +R+   I+ EHGKT+EDA GEL RGIENVEYA    ++LK
Sbjct: 61  PPAKRARVMFRFRQLLEDNADRVCAAITREHGKTLEDARGELTRGIENVEYACGIADLLK 120

Query: 120 GEYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPS 179
           GE+S+NVGP ID+WS+FQP+GVVAGITPFNFPAMVPLWM+P+A+ACGN FILKPSERDPS
Sbjct: 121 GEHSKNVGPGIDSWSEFQPLGVVAGITPFNFPAMVPLWMFPVAVACGNCFILKPSERDPS 180

Query: 180 STLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKR 239
           ++LL+A+L  EAGLP GVLNVVHGDK AVD L+  P V+A+SFVGSTP+AEY+Y+ GT  
Sbjct: 181 ASLLVAQLAQEAGLPPGVLNVVHGDKEAVDTLLTDPRVQAVSFVGSTPVAEYVYATGTAH 240

Query: 240 GKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQ 299
           GKRVQALGGAKNHA++MPDADLDNAVSA+MGAAYGSCGERCMAISV V VGD  AD +V 
Sbjct: 241 GKRVQALGGAKNHAIVMPDADLDNAVSAIMGAAYGSCGERCMAISVVVAVGDATADRVVA 300

Query: 300 KLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHE 359
            L  Q++ LK+GAGT  G DMGPLVT A  +KV G++D GVA+GAELVVDGRG  V GHE
Sbjct: 301 MLAEQVRSLKVGAGTGAGCDMGPLVTRAHFEKVKGFVDQGVAEGAELVVDGRGLVVPGHE 360

Query: 360 NGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDG 419
            GFFLGG LFDRVTP+M IY+EEIFGPVLC+VRV +++E M LI+ HEYGNGTC+FTRDG
Sbjct: 361 GGFFLGGCLFDRVTPDMRIYREEIFGPVLCVVRVATMQEGMDLIDAHEYGNGTCLFTRDG 420

Query: 420 EAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQ 479
           EAAR F D I+VGMVG+NVPLPVPV+YHSFGGWKRSLFGDL AYGPDGVRFYT+RK ITQ
Sbjct: 421 EAARYFTDAIKVGMVGINVPLPVPVSYHSFGGWKRSLFGDLAAYGPDGVRFYTRRKTITQ 480

Query: 480 RWPQRKSHEAAQFAFPS 496
           RWP     E AQF+FPS
Sbjct: 481 RWPTGGVREGAQFSFPS 497


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: 851
Number of extensions: 28
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: 498
Length of database: 499
Length adjustment: 34
Effective length of query: 464
Effective length of database: 465
Effective search space:   215760
Effective search space used:   215760
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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