GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Caulobacter crescentus NA1000

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= reanno::Smeli:SMc00781
         (498 letters)



>FitnessBrowser__Caulo:CCNA_03243
          Length = 499

 Score =  207 bits (526), Expect = 9e-58
 Identities = 146/466 (31%), Positives = 231/466 (49%), Gaps = 27/466 (5%)

Query: 8   IDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAA--QPKWAATNPQRR 65
           IDG  V   SG   +  +P  G+V   V      D+  AV  A+AA    +W    P+++
Sbjct: 25  IDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQK 84

Query: 66  ARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKG-DIVRGLEVCEFVIGIPHLQKSEFT 124
             V  +  +L+  + +ELA + S + GK I DA+  DI   +  C +      L K    
Sbjct: 85  KAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEA--LDKVYGE 142

Query: 125 EGAGPGIDM-YSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVPI 183
            G  P   + Y++ +P+G+   I P+NFP  + MW  APA+A GN+ +LKP+E+ P   +
Sbjct: 143 VGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTAL 202

Query: 184 RLAELMIEAGLPAGILNVVNGDKG-AVDAILTHPDIAAVSFVGSTPIARYVYG-TAAMNG 241
           +L  L +EAGLP G+LNV+ G  G A +A+    D+  ++F GS P+ R +   +A  N 
Sbjct: 203 KLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSNL 262

Query: 242 KRAQCFGGAKNHMIIMPDA-DLDQAANALIGAGYGSAGERCMAIS---VAVPVGEETANR 297
           KR     G K+  I+  D  DL+ AA A     + + GE C A S   V  P+ +    R
Sbjct: 263 KRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAFLAR 322

Query: 298 LIDKLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQ 357
           +I+    + + +++G   D     G +V++         I +   QGA+ V+ G+  +++
Sbjct: 323 VIE----VAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQ--RVR 376

Query: 358 GYENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYT 417
               G ++   +FD V PD  + + E+FGPVL V+   + +EA+ L     YG    ++T
Sbjct: 377 QEAGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWT 436

Query: 418 RDGDAARDFASRINIGMVGVN----VPIPVPLAYHSFGGWKSSSFG 459
            D   A   A R+  G+V VN      I +P     FGG+K S FG
Sbjct: 437 ADVSKALRGARRLKAGLVWVNGWDACDITMP-----FGGFKQSGFG 477


Lambda     K      H
   0.319    0.137    0.409 

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: 523
Number of extensions: 25
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: 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:

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